Does Current Biology have the Misfortune of Owning an Unreliable Clock?
Bhakti Niskama Shanta, Ph.D.
Sri Chaitanya Saraswat Math, New Pal Para (Netaji Sarani), Hayder Para, Siliguri – 6, West Bengal, India.
Email: email@example.com, Phone: +91-3532592004 (L), +91-9748906907 (M)
The archaeological record is very limited and its analysis has been contentious. Hence, molecular biologists have shifted their attention to molecular dating techniques. Recently on April 2013, the prestigious Cell Press JournalCurrent Biology published an article entitled “A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes”. This paper has twenty authors and they are researchers from the world’s top institutes like Max Planck Institute, Harvard, etc. In the present article the author discusses a few significant fallacies of the methodology employed by this paper in Current Biology.
The introduction to this Current Biology paper begins with:
Differences in DNA sequences correspond to nucleotide substitutions that have accumulated since their split from a most recent common ancestor (MRCA). When the average number of substitutions occurring per unit of time can be determined, the ‘‘molecular clock’’ rate can be estimated. Under the assumption of constant rates of change among lineages, molecular clocks have been used to estimate divergence times between closely related species or between populations. Fossil evidence has been frequently used to estimate a date for the MRCA of two related groups, thus providing a calibration point for the molecular clock. The sparseness of the fossil record, however, poses limitations on the reliability of such estimates. For example, in human evolution, no fossil has yet been identified to represent the uncontested MRCA for humans and chimpanzees or other closely related primate species. As a consequence, the nuclear and mitochondrial mutation rates for the human lineage have been heavily debated.
Respected authors of this paper have emphatically accepted that the fossil record is inadequate and unreliable. These statements clearly substantiate that now biologists are agreeing that fossil records do not provide any significant evidence at all for conventional evolution theory. Despite the well-recorded fact of the continual grand propaganda of Darwinism based on fossil evidence for more than 150 years, in recent times biologists are surprisingly coming up with such statements, based on their confidence that evolution can be explained purely by the genealogical/genomic record provided by modern molecular biology. Still many respected journals (for example the Nature) continue to publish articles on fossil evidence to support Darwinian evolution. These incoherently diverse claims prove that Darwinists are struggling with unscientific ideological approaches to explain biodiversity. The author of the present article highlighted these points in his paper “A Scientific Basis for Vedāntic View of Biodiversity” published in the February 2013 issue of the Newsletter The Harmonizer. In that article the author elaborated the problems associated with the fossil record and dating techniques, and its implication on the neo-Darwinian mechanistic misconception of biological life as mere molecular chemistry or abiology. The article in The Harmonizer was an abridged version and the full article is also available online. Very recently the author presented a part of that paper at Indian’s premier institutes like IIT-BHU, Allahabad University and IIT-Kharagpur. To convey these scientific facts among prominent scientists in India on this field, the author will be presenting a similar paper entitled “Modern Geological Evidence Undermines the Chronology of Geologic Column” in the upcoming conference: 18th Convention of Indian Geological Congress & International Symposium on “Minerals and Mining in India-The way forward, inclusive of cooperative mineral – based industries in SAARC countries”, from 27th – 29th April 2013 at M. P. Council of Science and Technology, Vigyan Bhawan, Nehru Nagar, Bhopal, Madhya Pradesh, India.
Coming back to the Current Biology paper, the introduction of the paper also states:
Recent analyses of de novo substitutions from genome sequencing of parent and offspring trios allow the direct calculation of nuclear substitution rates per generation. This alternative to the fossil calibration of the human molecular clock is arguably more accurate. Surprisingly, publications using this approach have recently pointed to de novo rates that are about half the value of those previously determined from fossil calibrations.
This further establishes that not only is the fossil record unreliable but also two methods (Phylogeny-based and Pedigree-based) used in the human mitochondrial molecular clock are also not in agreement with each other. Let us understand first what is ‘mitochondrial molecular clock’ and how it works.
Mitochondrial Molecular Clock (MMC)
Mitochondria are the energy-producing sections of the cell. Mitochondria extract energy from food molecules floating in the cytoplasm outside the nucleus of the cell and covert that energy into ATP. Hence, mitochondria are the important organelles of cells, without which biological processes would collapse. Mitochondria have their own DNA (mtDNA) and they are located outside the nuclear DNA. Believing that mtDNA (contains around 97 genes) is much simpler as compared to the cell’s nuclear DNA (contains around 60,000 genes), biologists try to build the Mitochondrial Molecular Clock (MMC) by making two oversimplified assumptions: (1) MtDNA is only passed down along the matrilineal line, and (2) mutations in mtDNA occur at a statistically uniform rate. We will discuss below the unscientific nature of these two over-simplified assumptions. The schemes employed in MMC dating are deceptively simple. Biologists believe that point mutations on a gene sequence represent copy errors and such errors build up randomly in due course. They think that the total sequence difference found between homologous genes of two taxa is a function of time since they have been diverted. It is important to note that MMC must depend on dating techniques which are used in the fossil record to determine the age of partition for one pair of taxa. Only after knowing the age of partition can the rate at which genetic change has occurred be estimated. Thereafter they simply extrapolate this data of one pair of taxa to date the times of divergence of other pairs of taxa. Hence, the techniques employed in MMC must depend on volatile calibration points and also there is no tangible way to establish accurate phylogeny with correct branching order and branch-length estimates.
Who is the human mitochondrial ancestor: Adam, Eve or both!
It is a general notion that paternal leakage is prevented in sexual reproduction because paternal mitochondria within the sperm are dynamically destroyed by the egg cell after fertilization. However, evidence started challenging this commonly accepted concept. Some studies report that the tail of the sperm, which have extra mtDNA, can successfully enter the egg. Numerous studies also report paternal mtDNA inheritance in animals, for example in the case of Mytilidae, sheep, Drosophila simulans and so on. These empirical observations directly invalidate the assumption that mtDNA is only passed down along the matrilineal line.
There is a Mitochondrial Eve hypothesis and it assumes that in humans all mtDNA can only be passed from mother to offspring without any recombination. Based on this unverified assumption, the Mitochondrial Eve hypothesis explains that mtDNA in every living person has directly descended from a hypothetical woman called Eve (named after Biblical Eve). According to this hypothesis all present humans came from Mitochondrial Eve. Thus biologists simply assume that mtDNA is passed intact from great-grandmother to grandmother to mother to daughter with virtually no input from males. In such assumption there is no mixing, no blending of father’s and mother’s genes and the reason for such assumption is that mixing can jumble, complicate, and thus obscure the history of mtDNA.
In order to maintain this view, past researchers believed that human paternal mtDNA is never transmitted to offspring. The concept of mtDNA inheritance from the maternal side only greatly simplifies the analysis and hence researchers use it to trace maternal lineage far back in time. MtDNA phylogenies, founded explicitly on the assumption of strict maternal inheritance, have been employed to narrate the story of Mitochondrial Eve, the hypothetical female who carried the last common ancestor of all human mtDNA. Based on this simplistic molecular clock analysis, researchers had explained that Eve was living in Africa 20,000 years ago. The same analysis is also extended to trace the lineages of other geographical locations, and in studies for European ancestry, female names (like Helena and Jasmine) have been given to these mtDNA based ancestors.
MtDNA can be a handy molecular tool for reconstructing evolutionary events only when the simplicity of its inheritance (maternal and without recombination) is valid. However, in recent times several studies report that paternal mtDNA transmission is possible in the case of humans and it also includes recombination similar to the cell’s nuclear DNA. In 1999 a study published in the prestigious journal Science states:
The assumption that human mitochondrial DNA is inherited from one parent only and therefore does not recombine is questionable. Linkage disequilibrium in human and chimpanzee mitochondrial DNA declines as a function of the distance between sites. This pattern can be attributed to one mechanism only: recombination.
In the same year, another article published in Science also highlighted this mixing of maternal and paternal mtDNA in humans and chimpanzees. Consequently many such studies have established recombination in human mtDNA. In 2004 Ladoukakis and Eyre-Walker summarized the situation:
Over the last 5 years, there has been considerable debate as to whether there is recombination in human mitochondrial DNA (mtDNA) (for references, see Piganeau and Eyre-Walker, 2004). That debate appears to have finally come to an end with the publication of some direct evidence of recombination. Schwartz and Vissing (2002), 2 years ago, presented the case of a 28-year-old man who had both maternal and paternally derived mtDNA in his muscle tissue – in all his other tissues he had only maternally derived mtDNA. It was the first time that paternal leakage and, consequently, heteroplasmy was observed in human mtDNA. In a recent paper, Kraytsberg et al (2004) take this observation one step further, and claim to show that there has been recombination between the maternal and paternal mtDNA in this individual.
In 2008 an invited review in Molecular Ecology also highlighted the presence of paternal leakage, recombination and heteroplasmy and its impact on analyses based on mtDNA:
The power of mtDNA analyses derives from a relatively high mutation rate and the apparent simplicity of mitochondrial inheritance (maternal, without recombination), which has simplified modelling population history compared to the analysis of nuclear DNA. However, in biology things are seldom simple, and advances in DNA sequencing and polymorphism detection technology have documented a growing list of exceptions to the central tenets of mitochondrial inheritance, with paternal leakage, heteroplasmy and recombination now all documented in multiple systems. The presence of paternal leakage, recombination and heteroplasmy can have substantial impact on analyses based on mtDNA, affecting phylogenetic and population genetic analyses, estimates of the coalescent and the myriad of other parameters that are dependent on such estimates. Here, we review our understanding of mtDNA inheritance, discuss how recent findings mean that established ideas may need to be re-evaluated, and we assess the implications of these new-found complications for molecular ecologists who have relied for decades on the assumption of a simpler mode of inheritance.
The paper in Current Biology (that we have discussed in the beginning of this article) considers only maternal relatedness and completely ignores the paternal leakage. The paper states,
our data provide some support for maternal genetic continuity between the pre- and post-ice age European hunter-gatherers from the time of ﬁrst settlement to the onset of the Neolithic.
As the authors of this paper employed an outdated analysis which ignores paternal leakage, their conclusions are unreliable. The actual fact is that mtDNA analysis cannot explain who the human mitochondrial ancestor is: Adam, Eve or both.
Demise of uniformitarian belief about mutation rates in mtDNA
Uniformitarian thinking is the heart of Darwinism and hence Darwin’s objective evolution theory cannot survive without uniformitarian analysis. Darwin stated in chapter 6 of his Origin of Species “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case.” Neo-Darwinism or Modern Synthesis also followed the same doctrinaire approach, and for the past six decades Darwinists based their studies on the false assumption that inheritable novelty is the consequence of chance or slight accidental modifications or mutations. Towards the end of the first half of the 20th century, Darwinists established a molecular interpretation for this standpoint. The way DNA worked was translated into conventional evolutionary theory, and random mutations were considered as copying errors that changed the DNA sequence one base-pair at a time, and, as a result, protein sequences were changed one amino acid at a time. They believe that the organism has no control over the alteration process, and that the genome mechanically decides organism characteristics. For them genome is a ROM (read-only memory), which is modified only by accident. This claim of Darwinists about randomness and accident became dogmatic with the intent to reject all possible revivals of the role of a supernatural agent found in religious explanations as the cause of origin of diverse living organisms. However, with advancement of molecular biology it is observed that large parts of DNA alteration in bacteria and eukaryotes are a result of a coordinated accomplishment of natural genetic engineering. Hence, the traditional understanding of genome variation as stochastic events or unpredictable accidents is now replaced by a controlled and coordinated accomplishment of cellular biochemistry. Now we know that cellular biochemistry is based on guided mechanisms and thus acts in predictable ways. In contrast to Neo-Darwinism, DNA changes are now known as nonrandom with respect to time, physiology and life history. The emerging alternative view of 21st century biology explains the genome as a RW (read-write) memory system subject to nonrandom change by sentient cell functions. Lynn Margulis’ research also highlighted the importance of symbiogenesis in swift genetic alterations and hence directly challenged the Darwinian belief of gradual alteration. This paradigm shift is a major setback to uniformitarian-based Neo-Darwinism. The author of the present article discussed this topic with more details in one of his papers published in the November 2012 issue of The Harmonizer.
Uniformitarian thinking can be found in every aspect of Darwinism including the fossil record analysis. A typical stratigraphic column shows a series of sedimentary rocks, with the oldest rocks on the bottom and the youngest on top. Stratum is an essential fundamental element to study geologic time scale. Geologists, paleontologists and other earth scientists use the stratigraphic principle to describe the timing and relationships between events that have occurred during the history of the Earth. In the 17th century Danish scientist Nicolas Steno (1669) formulated the basic principle of Stratigraphy based on three major assumptions: (1) Principle of superposition, (2) Principle of continuity, and (3) Principle of original horizontality. Evolutionists recognize the age of the fossil according to the geologic time scale based on the vertical location of the strata in which the fossil was discovered. Based on Steno’s uniformitarian assumption, fossils obtained from the bottom of the geologic column are recognized by evolutionists as the most ancient fossils. Steno’s three basic assumptions on which stratigraphy stands were never substantiated by either experimentation or empirical evidence. French sedimentologist Guy Berthault could recognize the defects in Steno’s simplistic assumptions and carried out the most fundamental experiments on sedimentation in Colorado State University with Pierre Julien (Professor of hydraulics and sedimentology) to invalidate Steno’s stratigraphy theory. In the February 2013 issue of The Harmonizer the author of the present article discussed the demise of this uniformitarian assumption based on a hypothetical representation of the Earth’s surface as an ‘onion skin’ with successive layers representing the events throughout the history of the globe.
The same uniformitarian assumption is also used for mutation rates to construct the so-called universal molecular clock. The first paragraph of the paper in Current Biology that we have discussed in the beginning of this article also states, “Under the assumption of constant rates of change among lineages, molecular clocks have been used to estimate divergence times between closely related species or between populations.” However, we know that such assumptions were discredited long ago. Instead, researchers reported a great deal of rate variation among loci on a gene, between branches on a tree and within single lineages over time. Researchers rigorously condemned the blind assumption of molecular rates of variation because they may lead to either underestimation or overestimation. This rate heterogeneity is a severe problem for precise evaluation of divergence times using a molecular clock.
Depending on the cell type, mammalian cells have a few hundred to hundreds of thousands of mtDNA. Even though the quantity of mtDNA seems to be firmly regulated in a tissue-specific manner, the quantity of mtDNA may change in due course through extremely complex regulatory mechanisms. Pathogenic mutations can abruptly influence a varying section of several mtDNA molecules and hence is the cause of heteroplasmy–the presence of a mixture of more than one type of mtDNA. The mutation rate can differ from person to person and even between adjacent cells within the same individual. The existence of heteroplasmic individuals in a sample may extremely obscure the estimation of mutation rates. Research also confirms that human mtDNA does not alter in a clock-like manner. Moreover, sufficient calibration points are absent for exact time estimates for human MMC. Hence the values of the mutation rate of human mtDNA differ significantly depending on the available data and the method used for estimation. These scientific facts and its impact on MMC are also ignored by the paper in Current Biology.
Faulty Fossil Record and Faulty Mitochondrial Molecular Clock!
Interestingly the paper in Current Biology states that,
Here we use the complete or nearly complete mitochondrial genomes from ten ancient modern humans for which reliable radiocarbon dates are available to calculate the human mtDNA substitution rate directly. This strategy circumvents the limitations imposed by the use of indirect measures of substitution rates such as those obtained via fossil calibration.
To overcome the problems in fossil record the authors used only a new term ‘direct method’ but in reality it is the same old radioisotope method commonly employed in fossil records. Hence the calibration of the molecular clock is again dependent on fossil data only. It is most important to note that the authors simply presume that radiocarbon dates are reliable. The author of the present article recently discussed the several problems that are associated with the radiocarbon dating and the full article is available online. In the Current Biology paper, the authors used samples within a span of 40,000 years of human history because they know very well that anything beyond 50,000 years will lead to a situation where it is not possible to find a sample with high enough concentration of C-14 (half-life period is merely 5,730 ± 40 years) to perform the tests. It is also a well-known fact that C-14 concentration in atmospheric CO2 often varies due to solar activity, geomagnetic field strength (Bucha, 1970) and numerous other factors. Due to these variations, the C-14 clock runs at a varying pace throughout the history of Earth, thus an unimaginable calibration would be needed to establish a relation between C-14 time and the anomalous MMC. Hence the use of carbon dating in the MMC of thousands of years is unrealistic. The MMC is based on erroneous assumptions and for its calibration it has to depend on the anomalous fossil record. Hence such methods are doubly deceptive and conclusions derived from such approaches must remain unstable.