2011 DNA Results
2003 vs 2011 Mitochondrial DNA Testing:
Early in 2011, the geneticist sequenced some fragments from the Starchild Skull DNA sample that, when examined by a program similar to BLAST, revealed they were segments of mitochondrial DNA rather than nuclear DNA. This was an intriguing development.
Up to that point, he had accepted the Trace Genetics result of 2003 (that the Starchild’s mtDNA was entirely human) as accurate. However, the primer series utilized in 2003 recovered only relatively small and quite specific segments of human mtDNA. The situation at that time left room for error and therefore should be clearly understood.
When the primers employed in 2003 found corresponding fragments on the Starchild’s mtDNA, the primers rendered a positive signal from the PCR indicating “this particular part of the mtDNA is human, or highly human-like.” However, that did not mean other untouched sections of the mtDNA would not vary considerably from the human mtDNA. And this, apparently, is what happened—the 2003 sampling proved to be too small.
2011 DNA Testing & Results:
Mitochondrial DNA is quite distinct from nuclear DNA. While both mtDNA and nuDNA exist as double-strand molecules forming the famous “double helix,” nuDNA is segregated into 46 chromosomes (in humans). Due to the massive amount of DNA in chromosomes (each consisting of millions of base pairs), DNA is tightly packed into multiple folds and is encased in a shell by large amounts of proteins called histones.
In contrast, mtDNA forms a tiny circle consisting of 16,569 base pairs. Despite its small size, its function is crucial to life. In the entire course of human existence, our mtDNA has accumulated only 120 ± variations across the entire population. Compare that to nuDNA, whose 3 + billion base pairs have as much as 15 million variations between individuals.
Human mtDNA contains 37 genes, 15 of which are larger and depicted above, and 22 of which are tiny bits of transport RNA (tRNA) not included. Of the 15 larger, 2 encode for mitochondria-specific RNA (ribonucleic acid) that constitutes a crucial component of mtDNA’s protein-making machinery (called ribosomes), but does not actually encode proteins. That is carried out by the 13 other large genes in the mtDNA, which do encode proteins for the production of energy and other critical functions of the mitochondria.
Mitochondria are the power plants of all cells that contain them, with a similar function in the biology of all species on Earth. MtDNA is one of the most thoroughly researched and well-understood aspects of human genetics. The coding capacity of mtDNA is used very efficiently, having exactly enough genes to carry on its job of producing proteins.
Since the beginning of eukaryotic cells (those with a nucleus) around 2 billion years ago, the mitochondria in them have carried out the most fundamental aspects of sustaining life. This has been true from yeasts to dinosaurs to humans. Their critical functioning is why very few differences are found between the mtDNA sequences of closely related species.
Mutational change in the human mtDNA nucleotide sequence is exceptionally rare (only 120 ± among all humans), and each mutation is well documented. The chart below is a screen capture of the output from a computer program that compares the entire mtDNA sequences of 33 different human haplogroups, one sequence for Neanderthal, and two for the recently discovered Denisova type of hominid. This output is called DNA alignment.
At the top, highlighted in dark blue, is the Human mtDNA Control Reference Sequence (CRS), which represents the sequences of one particular individual chosen as a reference, so everything else can be compared to that standard. The sequence depicted here starts at nucleotide #1255 (out of 16,569) and continues across to #1350. Notice this block of 95 nucleotides contains no variations in any haplogroup. Every base pair nucleotide is identical across all 33 groups of humans, the Neanderthal, and the two Denisova.
Both Neanderthal and Denisova have mtDNA more varied than human mtDNA, but they still contain many long unvarying segments. Neanderthals differ from the human CRS by 200 ± base pairs. The Denisova differ from it by 385 ± base pairs, which is why they are designated as separate from humans and Neanderthals. As a comparison, chimp mtDNA differs from the human CRS by 1,500 ± base pairs, as shown in the following graph.
MtDNA is so highly conserved because nature applies a very strong selective pressure against changes in its most critical regions. When changes do occur in such places, it can lead to disruption of a crucial activity, which can lead to dysfunction and death. As a result, an unfavorable mutation is not passed along. However, mutations that do not change proteins, and those in regions that do not encode proteins, can and do slowly accumulate.
This explains why only 0.0072% of human mitochondrial DNA has any variation across its 33 haplogroups. Below is an example of variation in human mtDNA. The haplogroup L1a has a C (cytidine) nucleotide, while at the same location all the other haplogroups have a T (thymidine) nucleotide. (The program’s output highlights all variations to aid researchers.)
Each variation like the one above is called a Single Nucleotide Polymorphism (SNP), and for human mtDNA such “snips” are catalogued in databases maintained by the NIH. The fewer substitutions a DNA segment has, the more conserved it is. Human mtDNA, with only 120 ± variations in 16,569 base pairs, is considered highly conserved.
Notice that the first haplogroup in the chart below the Control Reference Sequence (CRS) is haplogroup A (HPT A). This is the haplogroup that was matched to the human female skull found with the Starchild Skull. The next down is haplogroup C (HPT C), matched to the Starchild with small fragments of its mtDNA in 2003.
When Trace Genetics detected the Starchild’s mtDNA, they used human-specific primers that amplified segments of a few hundred nucleotides long. These segments were targeted for diagnostic analysis because they contained human haplogroup-specific changes that could determine whether mtDNA belonged (or not) to a specific haplogroup.
If the targeted segments also happened to be a part of a highly conservative sequence of human mtDNA that has a crucial biological function, the segments could be similar even among very different species (i.e., humans and chimps), leading to confusing conclusions.
In early 2011, our geneticist analyzed newly sequenced fragments from the Starchild Skull’s DNA samples. A computer program similar to the BLAST program mentioned earlier matched several Starchild fragments to catalogued fragments of human mtDNA.
One fragment matched a segment in the chart shown earlier, seen expanded below. This is a highly conserved segment of human mtDNA, with only 1 nucleotide variation among 33 human haplogroups present (L1b). There is also one in Neanderthal and one in Denisova .
This chart goes from #1262 to #1426 (164 nucleotides). Now imagine a line added across the top labeled “Starchild Skull” containing 167 nucleotides, but covering only 157 of the human mtDNA nucleotides to which it matched. Discrepancies like this (167/157) occur because the computer program is designed to find matches between two or more DNA fragments, in this case the human CRS and the Starchild Skull’s mtDNA. If it calculates that a sequence would match if more or fewer letters were in either code, it inserts gaps containing dashes to produce better aligned results, as seen in the diagram below:
In the comparison above, the first four letters match. However, at the fifth space a jumble would begin within the sample if the gap (containing a dash) was not inserted where it is. This is how the computer program works; it seeks to record the highest possible number of matches between two samples, so it inserts gaps, and each gap provides a negative penalty score as the program calculates the highest total of matches.
To make the Starchild’s mtDNA match the human CRS, the program added gaps marked as dashes either to the Skull’s mtDNA or to the CRS to obtain the highest matching score between them. Adding spaces to such misalignments in both samples provides a total cumulative difference, which in this case is a10-gap differential (167 – 157 = 10).
It is important to distinguish that adding gaps is not the same as outright changes in the nucleotides, as was seen earlier with the single C found in a row of Ts. Such changes are only one of three ways that differences are recorded when samples are being compared.
(1) The SNP just referenced is a substitution, when one nucleotide is replaced by another; (2) an insertion is when an extra nucleotide is found in a sample and the program has to introduce a gap into the other sequence to accommodate the extra nucleotide; and (3) a deletion, which is when a nucleotide is missing from one of the samples, and once again the program introduces a gap into the sequence to align it with the other sequence.
In the latter two cases, insertions and deletions, the program makes no distinction between which is the cause of the gap. All it does is insert the gaps into either sequence to keep the matching count as high as possible. Those gaps are called insertion-deletions, or indel(s).
Indels are clear points of variation between samples, but not all of them can be considered ironclad. All DNA testing requires multiple “runs” to be certain of every result. When the same sample is sequenced again and again, any of the three possibilities above might be corrected. Several runs will establish which variations can be catalogued as confirmed.
Now return to the Starchild’s 167 mtDNA nucleotides compared to 157 nucleotides of the human CRS in a highly conserved region where only one single variation is found in 33 human haplogroups. In such a strongly conserved area, multiple differences in a matched sample would immediately alert geneticists that something major might be unfolding.
Below is a screen shot of the 167 Starchild mtDNA nucleotides compared to the 157 in the human CRS. The top line of each row (highlighted in red) is the Starchild Skull sequence, which starts at 167 and works backward to 1. In the complementary Human CRS sequence (the second line of each row) the base pairs start at #1269 and end at #1426 (157 total) in the mirrored fashion mentioned earlier.
Within the 167 comparisons above are 17 variations! Seventeen! That is 17 indels of difference between the Starchild mtDNA and the mtDNA of 33 human haplogroups!
After repeated sequencing, some of those 17 differences could be confirmed as reading errors by the program, but it is virtually impossible that all of them would be errors.
What Does This Mean?
In any comparison of DNA samples between the human CRS and an “unknown” species (which technically categorizes the Starchild), even a few variations between them in a short stretch of highly conserved nucleotides strongly indicates that the entire mtDNA genome of that species would contain many more than the 120 ± carried by the human haplotypes.
Such a difference, which is not hypothetical but actually exists within the Starchild Skull, is by itself sufficient reason to suspect a new species has been identified! Clearly such an extraordinary claim requires extraordinary evidence, but the preliminary results achieved so far with the Starchild DNA are immensely encouraging, to the point of near certainty.
To calculate the exact percentage of difference between the Starchild Skull and humans will require its entire genome to be sequenced using sophisticated technology such as the machines provided by 454 Life Sciences and/or similar companies such as Illumina. We intend to perform that sequencing as soon as we have the financial ability to do so.
In the interim, our research team is releasing this report to focus on the 167/157 RNA segment of mtDNA because it is easy to understand. Several other mtDNA comparisons have been carried out, each much longer than that one, and three of those are depicted and analyzed in the Starchild Skull Essentials eBook (available HERE).
Remember that the information found by comparing mtDNA segments cannot and should not be considered thoroughly verified, as some sequencing errors are undoubtedly present. Each mtDNA segment must be sequenced several times to establish exactly how many differences exist between the Starchild Skull and the human CRS, and this kind of targeted testing, rather than shotgunning at random, is time-consuming and expensive.
Nonetheless, based on the preliminary results now in hand, our research team is very confident that when the Starchild’s entire genome is recovered and sequenced, the total number of confirmed differences will be so staggering that it can only lead to a conclusion that the Starchild represents an entirely new humanoid species, and that species is “alien.”
How could an “alien” have any human DNA, or even survive on our planet? Surprisingly, the genomes of many animal species have certain similarities (or homology) with humans. Proteins are the building blocks of all animal life on Earth, and the DNA that guides the production of proteins is very similar across all species. The genome of chimps is ± 97% the same as humans. Gorillas are 95% the same. Rats are 70%, mice 65%. Etc.
As mathematicians like to say, “Numbers don’t lie.” In this case, the 17 differences found in one short segment of Starchild Skull mtDNA makes it seem possible—even probable—that when the entire 16,570 ± nucleotides in the Starchild’s mtDNA are sequenced, they will contain far more than the 120 ± variations shared by the 33 human haplogroups.
Add to those 17 the number of differences found in three much longer fragments discussed in the eBook, and the total is mind-boggling. That number convincingly indicates that the Starchild will carry far more differences than the 200 ± of Neanderthals. It will carry far more than the 385 ± of Denisova. Could it possibly, or conceivably, reach the 1500 ± of chimps? Only further investigation will tell, but this is already a monumental discovery.
Source:
starchildproject.com/dna2011march.htm#8