Designer 101 for every evolutionist!

I have my own thoughts and response esp., on evolution and the arguments put forward in favour of it using genetics. In this post, I will address every argument put in favour 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 analysed 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 are 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 use. This is exactly why some genes are switched off or inactivated while others function.

As we know operating systems came a very 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 its 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 fewer 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 leftover 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 have 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, the code region, functions used, the data string used and the entry point.  However, none of these luxuries exists in genome reverse engineering. All we have is a sequence of code when executed has 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 the 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 the 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 at least see the computer word and understand in order to relate and detect design concepts. Evolutionary biologists are not designers or developers which are 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.

Why Evolution doesn’t fit the Quantum World: The Observer Effect

Many evolutionists and evolutionary biologists alike may have heard of a century old experiment called Double Slit Experiment. This is a high school experiment that proves that light can behave as a wave and a particle. But not all experiment results were not discussed in detailed in high school. What is missed could change the way everyone think what reality itself is. It’s called the observer effect.

So, what’s the big deal about Double Slit Experiment – the Observer Effect? Below is a quick video and I recommend you to watch it.



In short, light behaves like a wave as long as you don’t look at it. If you look at it, it behaves like a particle. The very act of observing makes light to behave like a particle. No one have a damn clue why light is behaving like a particle and a wave, and the wave equation is actually just a fluke. This experiment actually lays down the corner stone of the weird world of quantum mechanics. Going further into quantum mechanics, not all equations agree on a single universe. So, there was a multiverse proposed. While multiverse is gaining popularity, it is way to crazy to begin with because, the number of multiple universes that exists are the number of possibilities that can happen even at the electron level. The only other remaining explanation is the Copenhagen interpretation. Without going into details, it simply means, the knowledge of the observer collapses the wave function. So, what does it really mean and what does knowledge of something have anything to do with a particle? There is yet a good explanation not discussed at all – zeroverse. It is like nobody wants to talk about it, even though it is very obvious. It’s a simple concept that the entire world itself is a simulation. Why do I say that? I will take you through that experiment again: We believe that if we don’t watch something, it is still there. This is the classical view. But in reality, deep within microscopic quantum world, all particles exists as a probability – it isn’t there and it is also there. Which means, a particle can exist and cannot exist at the same time. However, the moment when someone watches it. the wave function collapses and becomes a particle. This is a solid scientific proof that we aren’t just materials of random chemicals but our very consciousness and the knowledge of a particle’s state collapses it’s probability. This cannot happen if we are evolved from a single celled organism. This can only happen if we are inside a simulated world.

I suggest everyone to watch the Google Tech Talks: The Quantum Conspiracy: What Popularizers of QM Don’t Want You to Know.



Hence, based on double slit experiment – observer effect, humans evolving from a single cell to a monkey and finally to humans is simply non-sense. It also doesn’t make any sense why something had to evolve in a simulated environment when humans who simply by observing can collapses the wave function and the way particles behave. Please note that double slit experiment – observer effect for quantum wierdness is not just for lights or electrons. Recently, molecules too produces interference pattern. (Ref: Largest Molecules Yet Behave Like Waves in Quantum Double-Slit Experiment)

True Age of mt-Eve based on Direct Pedigree Method

Since no one had taken effort to calculate the true age of mtEve based on the 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 words, 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 Cumberland gap-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 the 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 at least on average 8 mutations in HVR1 for RSRS.
One mutation can occur every 41 generations and humans have 8.5 mutations on average as the 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 mitochondrial 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 mitochondrial 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 Cumberland gap-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 the 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 at least 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 the 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 the coding region can be lethal, estimation based on the 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 becomes less. Hence, the overall estimation should be taken with a grain of salt must be taken well below the lower end, for the calculation that includes coding region.
Many scientists do acknowledge that the directly 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.

Update:

Criticism for the above post from a person with PhD in Population Genetics. Below email was forward to me to mention that I am wrong. I do not know who the person is as the person who forwards it to me didn’t reveal it to me. So, I am also not revealing any of the names here. For convenience, I will call the author of the below letter to John.

Hello ***,

Felix Chandrakumar really seems to be a troll exploiting the discrepancy between pedigree-based and evolutionary rates. As I understand, you need here, at first, a list of knowingly false statements of Mr Chandrakumar, rather than a discussion with the troll about these issues (e.g. admitting his ability to discuss the subject, his knowledge of basic literature published to date and his being a party in the discussion with the competence at least equal to that of authors of the papers he cites; NB! these authors never stated that evolutionary rates are useless or misleading, he does).

* He never goes into details of argumentation the authors engage. However, at least in Santos et al 2005 paper, many pitfalls of pedigree rates are discussed, among them: poor coverage of control-region-sites-known-to-mutate-evolutionary in all pedigree-based studies; inability to extrapolate what we know about the families where the data was collected, to the past; uncertail state of heteroplasmic mutations frequently found in pedigree studies.

* Mr Chandrakumar does not distinguish between mutation events of several different types. However, HVS mutations observed in pedigree studies are far from uniformity and only a portion of them can be directly compared to those employed in evolutionary studies. For instance, in the Costa-Rican study he cites I counted 3 phylogenetically informative mutations in 289 transmissions while he considers all 7 reported. If he reassesses the value of basic events in the mitochondrial molecule, he should supply the claim with appropriate arguments including data, simulations and math behind.

* The set of mutation observed in pedigree studies is a very small subset of all control-region sites known to mutate. Both sets clock and both can be used to estimate ages. What does he do when “revisiting” Eve’s age? Just applies his new rate (with confidence interval) to the age of Eve found by scientists and expressed in HVS mutation events. Which set was used by the scientists? The greater one. One with a mutation rate that cannot be estimated by pedigree studies, unless they lack an adequate funding. Narrowing the mtdna tree to the set of pedigree-estimated sites, we have to deal with a phylogeny with uncertain number of mutation events: for instance, positions such as 16095 of 16311 frequently found to vary in pedigrees, may quietly mutate 100 times in the way from any modern molecule to the Eve’s one, and only 10 of such changes, say, can be reconstructed in the tree. Even if the pedigree rate (10 times faster than one expected by the evolutionists) is the true rate for 16311 and similar sites, which tree we should use for the reconstruction? The tree now in use (one of Mannis van Oven, for instance) assigns the consensus state for such hotspots and doesn’t list the full set of their changes which appears to be unreconstructable. That’s the reason why most authors prefer coding-region estimations over control-region ones, at least for deep clades.

Nevertheless, even this small subset can be employed and useful, but with far more sophisticated techniques.

Regards
***

If you look at the criticism from a respected person with PhD on Population Genetics, who is from the scientific community, you will notice that in the first paragraph itself, two important points are well established.

  • Accepts the discrepancy between pedigree-based and evolutionary mutation rates
  • I am not fit to talk about it.

I will leave the “I am not fit to talk about it.” part because that shows his pride but that is not my concern. For some reason, he believes people in other disciplines cannot and/or will not be able to understand the scientific details of his discipline. As it much clear, the incapability is (falsely) primarily established in a deceitful manner to show that I disagreed with non-observable evolutionary mutation rates, pointing out that other authors agree on it.

Science is based on observation and experimentation. It is an accepted fact that non-observable evolutionary mutation rates (based on the human-chimp split) do not agree with observable direct pedigree mutation rates.

In the second paragraph, the tone of the statement “known-to-mutate-evolutionary” itself implies, no weight-age is given for observation in direct pedigree method, instead still assumes that evolutionary mutation-rate must be correct and one of the reasons for the disparity in mutation rates is because of the inability to extrapolate what they know about the families where the data was collected. It’s like saying, human/chimp must be true because I believe in it even though the observable evidence say contrary to it because that observable evidence must be wrong in some way.

In the third paragraph, as John says, let us consider only 3 mutations out of 289 transmissions, which gives a probability of 0.01038 (or 1 mutation every 96 generations). Hence, with 8.5 mutations from Eve, we have 96*8.5 = 816 generations. Taking 20 years per generation, the total age of Eve is only 816*20 = 16320 years, which is well within my conclusion. I don’t understand what John achieved by saying I took 7 mutations out of 289 instead of 3, even though all 7 are mutations. But still, 16320 YBP is nowhere near 200000 years mentioned for Eve using human/chimp split evolutionary rates.

In the fourth paragraph, I am amazed that John still insists in saying evolutionary rates as useful even though it greatly differs from observable evidence using the direct pedigree method. John then goes on to say that I am using the mutation rates which can be observed in direct-pedigree experiments which is much less and the scientists are using non-observable evolutionary rates which are greater. So, what is the true reason behind saying “coding-region estimations over control-region ones”? The coding region may not provide correct values in the direct pedigree method as we saw in the blog because the mutation in coding region is dangerous and the person may not survive giving an increased year if the coding region is included in the estimates. Hence, by wanting to use coding region estimates, what John is really saying, is to use evolutionary mutation rates because coding region estimates can be done only by assuming human/chimp split did happen.

I don’t understand how a mutation rate through observable direct-pedigree method does not have any weight-age over the non-observable human/chimp split based method. I thought scientists will disprove human/chimp split in evolution using the direct-pedigree experiment observations but rather, they all seem to twist the evidence and giving lame reasons like not knowing more about the families where data is collected. Shame on them!