I
am so upset that the reviews got leaked. That means I was once again
betrayed by an insider. On the up side, I feel a huge relief about it.
Now I don't have to sit on this horrible secret anymore. The world now
knows how unethically the scientific has behaved. It also knows that
we DID pass peer review and with reviews that came from geneticists that
work with whole genomes. At least that is what I was told.
Dr. Ketchum verifies the autheticity of the Peer Reviews via a post on her FaceBook page:
As far as all of the documents that were leaked, they are authentic. I didn't leak them though. Some submitters as well as others associated with the project had access to this information so I don't know who did. Those communications are not supposed to be leaked. So if anyone gets sued, it won't be me. They can subpoena the blogger's email trail. I actually am happy about the leak though. At least now everything I have said can be authenticated including the ridiculous and biased nature of the reviews. Now people will know the truth and that we did pass peer review
Dr. Ketchum's DNA Study the "Novel North American Hominins, Next Generation Sequencing of Three Whole Genomes and Associated Studies" did pass peer review in January 2013. The journal then known as the "Journal of Advanced Zoological Exploration in Zoology" (JAMEZ) gave the Ketchum DNA Study passing reviews and was planning to publish the study in its inaugural edition on or about January 11th, 2013.
Late in the evening of Wednesday January 9th, 2013 I received a phone call from David Paulides, Director of North American Bigfoot Search (NABS) the primary partner of the DNA Study. David informed me that he had just hung up the phone with Dr. Ketchum and she had been given notice that the DNA paper had passed peer review with JAMEZ and the publishing date "would be on or about Friday, January 11th, 2013". David said we should be prepared for some moderate media attention and possible interview request.
Then inexplicably the next day, January 10th, 2013, I receive the following email from David Paulides:
Apparently someone had gotten to the staff of the JAMEZ and intimidated them so severely that they were now refusing to publish the paper. Even the attorney for the JAMEZ was under so much pressure from some outside source that he had threatened to resign if the JAMEZ published the DNA study. (Editors Note: The above information was previously disclosed by Dr. Ketchum during radio interviews in February and March of 2013. This email is provided as independent collaboration of her claims made during these interviews)
To prove the journal did exist below is a screen shot of the JAMEZ's "Calls for Papers".
Later Dr. Ketchum acquired JAMEZ in order to preserve the passing per reviews. The JAMEZ was renamed Denovo (http://www.advancedsciencefoundation.org/). Dr. Ketchum then published the "Novel North American Hominins, Next Generation Sequencing of Three Whole Genomes and Associated Studies". Critics blasted her for doing this and claimed the paper never passed peer review. Due to confidentiality rules Dr. Ketchum could not make public the passing peer reviews from JAMEZ. Many critics, knowing these rules, used this against her and mounted an unprecedented personal smear campaign to discredit her and the DNA Study.
On Sunday, September 15th, 2013 I received a Facebook friend request from an individual I did not know. But since we had several "Facebook mutual friends" in common I accepted the friend request and did not think anything else about it. Late yesterday afternoon I received a Facebook message from this individual telling me he wanted my email address. He expressed his extreme dismay at the treatment I had received in the group "Bigfoot Community" the previous two days (http://www.bigfootevidence.blogspot.com/2013/09/ex-publicist-sally-ramey-opens-up.html) and was tired of the treatment I and the other supporters of Ketchum DNA Study had received over the past few months. He told me that he had inside information that would "Blow the lid off this thing and shut the critics up". He would not tell me what he had, he said "you will understand when you get my email". He also made me swear that I would keep his identity secret because the information he was giving me was "extremely sensitive". I gave him my email address and waited.
On Monday, September 16th I received his email. It contained a screenshot of an email from Scholastica, the publishing house for JAMEZ. Along with this screen shot I received the JAMEZ Peer Review with the authors' (Dr. Ketchum) responses and the Journal Nature's Peer Review from the second submission with authors' responses.
The email print screen that I received from the anonymous source clearly states that the Ketchum DNA Paper - "Novel North American Hominins, Next Generation Sequencing of Three Whole Genomes and Associated Studies" DID PASS A INDEPENDENT PEER REVIEW FROM A SCIENTIFIC JOURNAL. The status for the manuscript read: "ACCEPTED for publication with revisions" Below is the screen shot of the email:
Below is the JAMEZ peer review with Dr. Ketchum's (authors') responses that I received from the anonymous source. This is the peer review that was accepted for publication:
Authors’ Response to Review
Referee A
I appreciate having had the
opportunity to review this interesting investigation into such a controversial
subject and recognize the enormous constraints under which the authors and
their collaborators have labored.
Major concerns with this
manuscript:
1. A difficult two-part thesis
is posed that is inadequately substantiated by the analysis presented in the
manuscript. Both parts (i.e. Part 1 - previously uncharacterized hominins exist
in North America; Part 2 said hominins are the descendants of a putative
hybridization event involving an ancient uncharacterized hominin and a modern
human). A thesis this complex and counterintuitive requires significantly more
in-depth analysis and consideration and should be developed through a series of
peer-reviewed publications. Add in the idea that more than one species of
hominin may be present in North America and the effort to make a convincing
case is multiplied.
Author’s Response:
We removed the discussion of the
different variants of Sasquatch living in North America simplifying the
manuscript and added an alternative hypothesis outside of hybridization to the
discussion so further discussion of their origins can be fully developed in
future manuscripts. Lines 688-696.
2. The presentation of the
thesis is overburdened in three ways: a) the considerable inclusion of
unsubstantiated eyewitness accounts and folkloric/pop-cultural ideations and
their presentation as foundational facts that validate the analytical data; b)
the presentation of a series of anomalous results generated using routine
methodologies resulting in a sub-narrative that is curious and interesting, but
unnecessary given the fact that cutting edge technology has been employed to
generate sequence data sets that should allow for incredibly detailed analyses
yet lead to relatively unambiguous conclusions; and c) the results from Next
Generation Sequencing methodologies, especially related to the analysis of the
nuclear genome are fairly superficially treated so as to be unclear whether the
authors have selectively aggregated sequences to support a favorable placement
among primates. As stated in Perleman et al. (2011; PLoS Genet 7(3): e1001342.
doi:10.1371/journal.pgen.1001342, "...primate taxonomy is both complex and
controversial, with marginal unifying consensus of the evolutionary hierarchy
of extant primate species," and given the expertise of one of the authors
in this particular area, it is a bit astonishing that a more in-depth and
stepwise treatment is not provided. The decades of work published by the
Goodman lab provide an excellent roadmap for a convincing analysis. In summary,
this work would achieve a much higher degree of analytical credibility by a)
limiting folkloric/cultural references to the minimum necessary, b) moving many
of the references to anomalous results to a supplementary role (2nd
publication, perhaps), c) fully leveraging the treasure trove of information
yielded by the Next Generation Sequencing.
Author’s Response:
a) The
introduction with popular information was requested by another reviewer. Since there is broad interest in this
manuscript, that reviewer felt that the inclusion of such information was
important. I will leave it up to the
editor whether this should be included or not.
It should be noted that 2 of the authors of this paper did have
eyewitness encounters at the invitation of people that have interaction with
this species so it is not entirely unsubstantiated.
b) The
previous results were left in the manuscript because they supported the next
generation sequencing results and also because they were obtained from a large
number of purported Sasquatch samples, which behaved in the same manner as the
three samples utilized for Next Generation Sequencing.
c) The
purpose of the manuscript was to prove that the Sasquatch exist. We chose chromosome 11 as our starting point
for building our supercontig in order to generate the phylogenetic tree since
the scope of the manuscript was to determine whether a novel primate did exist
in North America. This was the logical
way to proceed and with the length of the contigs and also with more than 379
genes analyzed (for another manuscript in the future) we feel that this was the
direction to go to prove that they exist and as a preliminary study. In the beginning of the study, we had already
ruled out non-primate species with not only the mtDNA findings but also with
PP16 since it only gives results for ape and human with the exception of the
103 peak at Amelogenin that appears when there is animal DNA present in a
sample. The 103 peak was not found in
any of the purported Sasquatch samples that were screened using PP16.
Furthermore, fully leveraging the genomic data will take years. This manuscript is just the beginning of the
study.
3. A significant amount of work
leading to the generation of the data central to the thesis was outsourced. It
is very difficult to manage the quality control and release standards of
contract laboratories from the outside. This does not automatically call such
data into question. However, when coupled with a significant amount of
anomalous and ambiguous data, such concerns must be considered. This would be
especially true concerning Next Generation Sequencing of unknowns where
heterologous libraries may result from contamination. This technology is much
more sensitive to the detection of contaminating gene sequences than others,
and the possibility that contaminating sequences may affect the development of
a consensus sequence should be given considerable attention. Reference bias
should also be given consideration in the development of a consensus sequence.
Similar work typified by that of Pruefer et al. (Nature, 2012/06/13/online)
could provide good guidance concerning appropriate quality control analysis.
Author’s Response:
The outsourced laboratories were
accredited and work with human samples, which require regulation. We have correspondence where the laboratories
were confused about the results and in some cases doubled checked their
findings. Furthermore, more than one
laboratory repeated the analysis at least to some degree supporting the data of
other laboratories. They all utilized
the same extractions that had been aliquoted.
As far as the Next Generation data, it confirmed the mitochondrial
findings from previous laboratories as well as novel sequence. That is why it was important to leave the
original data in the manuscript.
Furthermore, according to supervisors in data analysis at Illumina, the
Q30 quality scores would have been remarkably lower if contamination had been
present in the genomes due to competition by the various sequences. That also would have affected the
mitochondrial findings which were consistent with the original mtDNA
sequencing.
4. Conflicting statements occur
concerning the validation against submitter contamination:
"Control DNA was obtained
from the majority of the submitters and was profiled using Promega PowerPlex®
16 (20). All submitters yielded complete profiles."
Author’s Response:
This has been corrected to
clarify on line 200: All submitters “tested”
At the very least the STR
profiles for the submitters of Samples 26, 31, and 140 should be presented, as
these samples yielded the most significant data of the study.
Author’s Response:
Since the submitters’ names are
given per their request contractually in Table 1, it would be inappropriate and
unethical to publish their DNA profiles as it would link to their identity. However,
we have them on file.
5. Sample 26 - It is stated in
the study that Sample 26 was derived from a shooting incident. The inclusion of
such a sample in the study may be inconsistent with contemporary scientific
ethics concerning the treatment of both human and animal study subjects and the
procurement of research specimens from such. Moreover, this description casts
the provenance of such a sample as murky, at best.
Author’s Response:
We have removed any references
to the alleged shooting incident. Line 481
6. The bioinformatics should
include gene sequences from expected outlier species that may also be capable
of contributing contaminating nucleic acids. For example, a BLASTN search using
Sample 26 does turn up some exceptionally strong homology with a gene from
Ursus americanus (DQ240386.1). This would support the idea that the consensus
sequence may have been affected by contaminant sequences.
Author’s Response:
There will always be some
homology with other species when short random sequences are chosen, however,
your example of bear contamination can be completely ruled out considering none
of the laboratories handling the samples have bear samples. Furthermore, forensic screening would have
given a 103 peak at amelogenin on PP16 should there have been non-primate
contamination. Sequencing of the
mitochondrial DNA with universal primers also would have shown any
contamination of the original extractions with non-human DNA. Additionally, that is a single isolate from
the black bear 7193328 brain-derived neurotrophic factor. Not only is it preset
in Sample 26, but it is just as present in Sample 140. Furthermore, DQ240386.1 is 489 bases. I wonder
why such a small sequence, ie 489 bases out of 2.7 million bases was the focus
of this critique. DQ240386 is
statistically significantly aligned with primates and carnivores. In fact, BLASTing DQ240386- ring tailed cats
of the raccoon family and seal have as much alignment as Ursus americanus. The
maximum score for raccoon and seal are about 850. Maximum score for Ursus americanus
is about 900. Max score for Sample 26 is 538. This shows contamination bias.
Minor concern
1. The use of “hominin” in the
introduction, as opposed to hominid, creates the perception of bias toward
folkloric and unverified eyewitness accounts that seem to emphasize human
characteristics. The general discussion of such creatures tends to split along
two lines: human or human-like and ape or ape-like. The term hominid, as
related to the Family Hominidae, is the higher order, and, thus, the broader
grouping. Visual description from a distance might allow for a reasonable
description of a hominid, but close examination of the organism or its remnants
is required for its placement into the Hominini. Thus, to establish initial
objectivity, the authors should use a qualifying adjective such as “putative.”
Author’s Response:
Pan/Homo
divergence occurred between 5.4 and 6.3 million years ago (refs below). Since the mtDNA speciation is not
only unequivocally modern human, but can be dated by the haplotypes obtained in
this study to as late as 13,000 to
26,000 years ago, these individuals must be included as hominins.
We
did add the word “putative” in line 85.
Bradley, B.J. (2006).
"Reconstructing Phylogenies and Phenotypes: A Molecular View of Human
Evolution". Journal of Anatomy 212 (4): 337-353. doi:10.1111/j.1469-7580.2007.00840.x.
Wood
and Richmond.; Richmond, BG (2000). "Human evolution:
taxonomy and paleobiology". Journal of Anatomy 197: 19–60. doi:10.1046/j.1469-7580.2000.19710019.x. PMC 1468107. PMID 10999270.
Referee B
1. This
is clearly important information that I hope the public will have access to
soon. However, I was immediately taken by surprise after thoroughly reading the
manuscript to see such a high reference to Hominins, including the title. I was
surprised because there is no substantial evidence presented by the author that
the species identified in the 3 whole genomes is a biped. Eye witness accounts
are the only data presented to determine or substantiate a biped of any kind.
It would be much more appropriate to delineate in this manuscript that novel
genomic evidence highly suggests an unknown species living contemporaneously in
the Continental and Subarctic United States and Canada within the Order:
Primate. There is no conclusive evidence that the unusual data found in the
follicular hair morphology or the tremendous genome results indicates a
"hominin". The tribe Hominini (of Homininae) is reserved for Homo,
post Panini divergence. Genetic information alone is not enough to classify the
species within a tribe or clad under order - Primate. Though there is
substantial alignment in some data relating to hair and other DNA studies, it
is too presumptuous to purport the extant data included in the manuscript
conclusively classifies this unknown species as hominin. An example (to the
author) of how to, perhaps, revise:
---The genomic data of sample
26 indicates the specimen allegedly collected from an unknown creature is
certainly novel and indicates an unknown species. The phylogenetic trees of
sample 26 indicate a species highly aligned with the order: Primate. If the
alleged story related to us by the hunter who submitted the sample, the species
is closely related to the hominin tribe because the hunter claimed to have seen
the creature walking "upright". Our chromosomal analysis would
substantiate a close hominini relationship. Further study and analysis will be
ongoing to determine such classification. The phylogenetic trees are quite compelling and
are probably the most substantial of the information given within the
manuscript. However, the information and data is not satisfactory to hypothesize
anything more than a living unknown primate. The molecular genetic data is
quite compelling and enough to publish in and of itself. But in order to use
taxonomic language in this manuscript, especially related directly to the
species itself- is inappropriate. In order to include the level of specific
taxonomy presented in the manuscript such as hominini, gross anatomical
evidence along with molecular physiological evidence must be included in the
manuscript. Even a clear video of this species actually walking bipedal would
give some sort of gross anatomical evidence. But eye witness accounts are not
enough to make such hypotheses. I do, however, believe the eye witness accounts
are important and should not be excluded. They are just not appropriate to
utilize for evidence to propose any hint of taxonomy, including hominini.
Author’s Response:
Pan/Homo
divergence occurred between 5.4 and 6.3 million years ago. Since the mtDNA speciation is not
only unequivocally modern human in 100% of the samples included in this study,
and furthermore, can be dated by the haplotypes obtained in this study to as
late as 13,000 to 26,000 years ago including the mtDNA from the 3 Next
Generation genomes, these individuals must be included as hominins. The human mitochondrial DNA haplotypes were
consistent between the Next Generation Sequencing and the original mtDNA whole
genomes sequenced in the beginning of this study.
1. Bradley, B.J. (2006).
"Reconstructing Phylogenies and Phenotypes: A Molecular View of Human Evolution".
Journal of Anatomy 212 (4): 337-353. doi:10.1111/j.1469-7580.2007.00840.x.
2.
Wood
and Richmond.; Richmond, BG (2000). "Human evolution:
taxonomy and paleobiology". Journal of Anatomy 197: 19–60. doi:10.1046/j.1469-7580.2000.19710019.x. PMC 1468107. PMID 10999270.
2. The
molecular genetics in this manuscript are the most important and it would be
important to include information regarding the analysis of the whole genomes.
The phylogenetic trees are exciting to look at and speculate about, but there
is not enough analysis to determine phylogenicity. I highly suggest including
language that 'it is recognized that continued analysis of the nuclear DNA will
be required in order to determine phylogenicity. The genomic information is
certainly impressive, but not as conclusive as the manuscript proposes. It is
inappropriate to make connections between the various samples. In fact, I
believe this weakens the manuscript due to the reality that the genomic data
and mtDNA analysis does not align well against each other (except for 2 of the
whole genomic sequences). There are similarities, and those similarities are
important to note. But conclusions cannot be drawn about the inter-relatedness
of these various samples. The number of samples do indicate high alignment with
Homo along chrm11. However, there are many other novel sequences across the
several samples that creates confusion for the reader. Perhaps it may be
helpful to split the manuscript up into several different studies- or simply
divide the manuscript up into major sections to delineate the different
evidenciary aspects. But to attempt to make links between the hair samples and
the novel genomic sequences and other DNA evidence is premature. Tremendous
work would need to take place with substantial evidence, including gross
anatomical evidence, to make such linkages between the various samples in the
study.
Author’s Response:
Mitochondrial
DNA has been universally utilized to determine species by the scientific
community. Since the mtDNA in Sasquatch
is not only unequivocally modern human in 100% of the samples included in this
study, that places the Sasquatch as human.
However, since the nuDNA is novel to a large extent, the speciation of a
potential progenitor is what is in question, especially since there are gene
sequences that align 100% with human interspersed in the nuclear genome.
3. The
other major problem with this manuscript is, again, the alleged specimens these
samples came from. It is important to state the samples came from alleged
Sasquatch specimens, which is done well throughout the manuscript, but not
consistently. It would be helpful, however, to include additional evidence to
corroborate the theory that the samples came from a large non-human biped.
Video evidence of this species walking bipedal would be important to help
strengthen the manuscript. In addition, it is inappropriate to make statements
regarding the dynamic between Homo Sapien DNA and the whole genome sequence. It
is appropriate to include statements about distant relationships with the
order- Primate. But it is certainly premature and the evidence is not
conclusive enough to make such close connections between this unknown species
and Homo Sapiens. I do believe that there is strong data in the whole genomes to
suggest alignment with Homo Sapiens. However, there is not enough evidence to
make statements about hybridization events. Hybrid phenomenon across the
Homo/Pan/Gorilla taxonomy are currently highly debated in the scientific
community. Making such claims is far too premature for a manuscript like this.
The manuscript demonstrates a universal bias toward a hominini hypothesis. This
anthropomorphic bias is problematic for this manuscript. A scientific
manuscript is intended to present facts, not biases. If the editorial board
decides to publish this manuscript with such a clearly "hominid"
favoured bias, they certainly should proceed, but I recommend doing so with a
strong disclaimer that an authored bias does exist in the manuscript.
Author’s Response:
Since the mitochondrial DNA
places them as human, in both the original sequencing of the mitochondrial
whole genomes as well as the Next Generation Sequencing, it is not premature to
align them with Homo. We did add another
hypothesis in addition to the hybridization theory on lines 692-696. In
consideration of the mitochondrial whole genomes, these are the only two viable
hypotheses available.
5. The
inclusion of the Q30 scores was very important for the author(s) to do. This
data strengthens the manuscript more than anything else included (if editors
wanted to publish based on the Q30 scores alone, then there would be no reason
not to publish). Furthermore, I am also most impressed with the presentation of
the phylogenetic trees for the 3 whole genomes. They clearly identified primate
relationships and alignment- though sample 31 seems to be very different from
the other two whole genomes. That is concerning and confusing. It may make more
sense to remove sample 31 altogether until the study can further understand and
explain the huge difference with sample 31 (including conclusive evidence, not
speculation). I am also pleased with the inclusion of the high definition
pictures of human hair morphology versus the unknown species comparison.
However, it would strengthen the manuscript to cross reference human morphology
so as to substantiate the statements regarding the comparisons. I am also
pleased to see the substantial amount of data and work taken to ensure high
quality DNA samples with clear and appropriate techniques
Author’s Response:
References 15-19 refer to hair analysis and
human hair morphology as well as animal hair analysis. As far as Sample 31, it should be included
because it has the same characteristics as all of the other samples, human
mitochondrial DNA and novel primate sequence in the genome as well as human
sequence. In the original manuscript we
discussed that eyewitness accounts clearly note physical differences related to
geographic location in North America. We
feel that 31 is such a variant. We had
taken this information out of the manuscript but will re-introduce it if
requested. The fact that overall, the
genome is consistent with the others as far as its makeup clearly establishes
its place in the manuscript.
6. The
pictures included thus far of a supposed creature that is claimed to be a
Sasquatch is of terrible quality and should be replaced with much more clear
photographic evidence or video. These pictures weaken this manuscript. The
inclusion of an image of sticks being put together in some kind of pyramid is
inappropriate. I would strongly suggest removal of this image.
Author’s Response:
We included the stick structure
because one of the samples (168) was obtained within this structure. Not only did this document chain of custody
for this sample but the fact that a viable sample was found within the structure
supports the discussion of eyewitnesses encountering unusual stick structures
within areas purported to be inhabited by the Sasquatch. As far as video, we are including
Supplemental Video 1 of a juvenile female Sasquatch sleeping. This video is from the Sasquatch that Sample
37 was obtained from which also lends credibility and chain of custody to that
sample. The still photos have been
removed from the manuscript with the exception of Figure 4 which has now been
edited to tie it to Supplementary Video 1 on lines 109-110 since the video is clearer
and in hi def.
Author Responses to
Referees 2
Referee
#1 (Remarks to the Author):
Comments re: The sasquatch genome project
1. Firstly - I reviewed a previous version of this ms and am pleased to see that the authors have wholly restructured their ms (it is now substantially improved, with many tangents and irrelevant areas of discussion removed or substantially modified). The previous version was rather opaque - was it dealing with sasquatch or not? I am pleased to see that this new version is bolder and more direct. However, does it present satisfactory data, and include satisfactory analysis of that data?
Given that much of the analysis and discussion concerns genetics, and given that I'm not a geneticist, my general feeling is that any decision about the fate of this ms must fall 'into the lap' of geneticist reviewers. Based on more general issues discussed here, I conclude that the work currently suffers from some areas of obfuscation that prevent me from understanding exactly what it is the authors are proposing. I therefore cannot recommend publication at the moment: if relevant geneticists argue for rejection of the ms, I would concur with this opinion. I admit to being greatly intrigued by the data being presented, however, and (as per last time) wonder if there is a 'Nature-worthy signal' in here somewhere.
The discussion early on of "high quality complete genomes" and so on sounds impressive, and I hoped to be impressed by the data collected and analysis of it. However, right out of the gate (1st line of abstract) we are told that the tissue samples concerned "were obtained... from... Sasquatch". This is problematic - the authors should state that the tissue samples were hypothesised to be from sasquatch, since the tissue samples were not collected directly from animals themselves: the project is testing the hypothesis that the samples come from an unidentified hominid.
Comments re: The sasquatch genome project
1. Firstly - I reviewed a previous version of this ms and am pleased to see that the authors have wholly restructured their ms (it is now substantially improved, with many tangents and irrelevant areas of discussion removed or substantially modified). The previous version was rather opaque - was it dealing with sasquatch or not? I am pleased to see that this new version is bolder and more direct. However, does it present satisfactory data, and include satisfactory analysis of that data?
Given that much of the analysis and discussion concerns genetics, and given that I'm not a geneticist, my general feeling is that any decision about the fate of this ms must fall 'into the lap' of geneticist reviewers. Based on more general issues discussed here, I conclude that the work currently suffers from some areas of obfuscation that prevent me from understanding exactly what it is the authors are proposing. I therefore cannot recommend publication at the moment: if relevant geneticists argue for rejection of the ms, I would concur with this opinion. I admit to being greatly intrigued by the data being presented, however, and (as per last time) wonder if there is a 'Nature-worthy signal' in here somewhere.
The discussion early on of "high quality complete genomes" and so on sounds impressive, and I hoped to be impressed by the data collected and analysis of it. However, right out of the gate (1st line of abstract) we are told that the tissue samples concerned "were obtained... from... Sasquatch". This is problematic - the authors should state that the tissue samples were hypothesised to be from sasquatch, since the tissue samples were not collected directly from animals themselves: the project is testing the hypothesis that the samples come from an unidentified hominid.
Authors’ Response:
Though a number of the samples were
taken immediately after eyewitness sightings of Sasquatch, we did change the
verbiage to correct this, Line 36, “hypothesized to be” from Sasquatch.
2. The comment, also appearing early on in the ms (p. 4), that the DNA evidence reveals "human DNA interspersed with sequence [data] that is novel and distantly related to primates" raised my eyebrows - what do the authors mean by this? That sasquatch, if imagined to be verified as real, is a hybrid of human and non-primate ancestry? Non-primate? I was interested in seeing this qualified: does it stem from a misuse of the term 'primate'? (I think we all agree that humans are primates).
2. The comment, also appearing early on in the ms (p. 4), that the DNA evidence reveals "human DNA interspersed with sequence [data] that is novel and distantly related to primates" raised my eyebrows - what do the authors mean by this? That sasquatch, if imagined to be verified as real, is a hybrid of human and non-primate ancestry? Non-primate? I was interested in seeing this qualified: does it stem from a misuse of the term 'primate'? (I think we all agree that humans are primates).
Authors’ Response:
Line 59: Corrected to read: human DNA interspersed with
sequence that is novel but primate in origin.
3. It is further stated on p. 27
that phylogenetic results "indicate distant relationships with multiple
primate sequences". Again - what exactly do the authors mean here? This is
never explained and I regard it as a major problem - the universally favoured
hypothesis (as made clear elsewhere in the present ms) is that sasquatch (if
real) is a primate, and specifically a hominoid, and presumably a hominid, a
hominine and perhaps a hominin, so the text creates the impression that a
non-primate ancestry is being preferred. Or, again, is this because 'primate'
is being used to mean 'non-human primate'?
Authors’ Response:
We
omitted the word distantly in Line 584.
The novel primate lineage comes off in the non-human range even though
there are human sequences interspersed in the genome. So, we were referring to
non-human primate.
4.
I was hoping that this would be clarified by examination of the
phylogenetic/gene trees. While I'm pleased that several phylogenetic/gene trees
have been included, they desperately need redesigning, since the text on the
branches is so small that it can't be read without exceptional magnification.
As such, the trees are essentially useless.
Authors’ Response:
We have attempted to enlarge them
but in PDF, they can be enlarged in Reader. We are still trying to make them easier to
read and currently have them at a publisher attempting to enlarge them without
changing the actual data and distance tree.
4. I appreciate that the authors have apparently tried to include as much data as possible in this ms. I would say that the photographic evidence (Fig 4A and 4B) should not have been included, since those images are poor in quality, do not appear compelling, and weaken the credibility of the ms. Scientific names are written incorrectly on p. 23.
4. I appreciate that the authors have apparently tried to include as much data as possible in this ms. I would say that the photographic evidence (Fig 4A and 4B) should not have been included, since those images are poor in quality, do not appear compelling, and weaken the credibility of the ms. Scientific names are written incorrectly on p. 23.
Authors’
Response:
We
removed the still of 4A and relabeled 4B as Figure 4. Supplementary video 1 shows the same
Sasquatch in greater detail and in high definition and therefore supports the
use of Figure 4, however if requested, we will remove 4 also. Since this individual is the donor of Sample
37, we felt that tying her to a photo and video was important. We will remove Figure 4 if the editorial
board or the reviewers believe that it should be removed after this
explanation. Lines 584 through 586 were
corrected as far as the scientific names.
Referee #2 (Remarks to the Author):
Short list of some scientific problems:
Short list of some scientific problems:
1. Repeated and abusive use of vague terms such as "multiple", "numerous", "many" or strange scientific terms such as "anomalous", "strinking", "unexplained" or "unexpected".
Authors’ Response:
The
words “multiple”, “numerous” and “many” were either removed or greatly reduced
in their usage. "Anomalous", "striking",
"unexplained" and "unexpected" were completely removed from
the manuscript.
2. There is a complete lack of statistical evidence or referenced scientific
work for the hair analysis; claiming "they were strikingly distinct from
human hairs" without any reference or evidence beyond this bold,
authoritative statement is not acceptable.
Authors’ Response:
References 15-19 refer to the hair
analysis. Figure 5 illustrates the differences between Sasquatch hair and human
hair. Materials and Methods also discuss
the methods utilized for hair analysis.
Statistics are not utilized in forensic hair analysis.
3. The vagueness of the extraction procedures is also surprising (how the contamination was minimized or DNA recovery maximized?): "The DNA was extracted in a clean room using forensic science procedures that minimized contaminant DNA in the samples while maximizing DNA recovery."
Authors’ Response:
The Material and Methods were
supplemental due to the length of the paper and it was stated in the manuscript.
The extraction techniques were discussed at length in the Supplemental
Materials and Methods.
4. Some paragraphs are confusing and again, the use of terms such as "clearly" or "as expected" is strange. "Control DNA was obtained from the majority of the submitters and was profiled using Promega PowerPlex16 20. As expected, all submitters yielded complete profiles. In contrast, when the hominin samples were tested using Promega PowerPlex16, partial profiles were evident in almost all cases. These data clearly showed that the samples were not contaminated by their submitters." (how?)
4. Some paragraphs are confusing and again, the use of terms such as "clearly" or "as expected" is strange. "Control DNA was obtained from the majority of the submitters and was profiled using Promega PowerPlex16 20. As expected, all submitters yielded complete profiles. In contrast, when the hominin samples were tested using Promega PowerPlex16, partial profiles were evident in almost all cases. These data clearly showed that the samples were not contaminated by their submitters." (how?)
Authors’ Response:
The words clearly and as expected
were removed. Lines 265 and 266 were
edited “These
data showed that the samples were not contaminated by their submitters since
all of the submitters’ profiles excluded as being a contributor to the hominin
profiles/partial profiles.” to show how the samples were not contaminated by
the submitters.
5. The authoritative and unsupported statements follow along the paper: "In the experience of this laboratory, hair samples constitute a very reliable source of DNA."
Authors’ Response:
We had previously had the following
in the paper but when we revised it, we discarded it due to the increased length
of the manuscript, however, we have reentered it into the manuscript, Line 280-283:
“Almost all large animal breed registries utilize plucked hair samples as their
primary source of DNA for their parentage testing programs. One horse
registry alone processes over 100,000 hair samples per year. These hair
samples are archived and are viable for many years after they are
submitted. Therefore the hominin samples were well within our
expectations as far as nuclear DNA yield and quality”.
6. Some methodologies are totally unspecific and uninformative: "After extraction, yield gels with 3 L of the extracted DNA were utilized to determine if there was DNA present and whether it was degraded".
6. Some methodologies are totally unspecific and uninformative: "After extraction, yield gels with 3 L of the extracted DNA were utilized to determine if there was DNA present and whether it was degraded".
Authors’ Response:
The Material and Methods discuss
this and it is visualized in Figure 7. Yield gels are a well established method for
visualizing not only the quantity of DNA in an extraction but also the quality
of the DNA since DNA will “smear” on a gel instead of giving a distinct band if
the DNA is degraded. Mild degradation is
depicted in Figure 13 with the human control that had been purposely degraded
prior to extraction.
7. More vagueness (we don't know how many samples are all): "All of the screened samples revealed 100% human cytochrome b and hypervariable region 1 sequences".
7. More vagueness (we don't know how many samples are all): "All of the screened samples revealed 100% human cytochrome b and hypervariable region 1 sequences".
Authors’ Response:
Line 317 changed to “All
110 screened samples”.
8. More methodological problems; in degraded DNA, artifactual amplifications are expected and potentially undescribed alleles have to be sequenced to see what's in the PCR product. "PowerPlex16 amplification of the hominin samples yielded only partial profiles with off-ladder alleles while amplification of DNA." ents : "Once it was established that the Sasquatch nuclear DNA did not conform to human DNA.."
8. More methodological problems; in degraded DNA, artifactual amplifications are expected and potentially undescribed alleles have to be sequenced to see what's in the PCR product. "PowerPlex16 amplification of the hominin samples yielded only partial profiles with off-ladder alleles while amplification of DNA." ents : "Once it was established that the Sasquatch nuclear DNA did not conform to human DNA.."
Authors’ Response:
The DNA was not degraded as we had a yield gel
of the raw DNA showing clear bands (Figure 7) not smears. As some of us are
forensic scientists, we are expert in determining DNA quality and mixture
(contamination) interpretation and the interpretation of PP16 which we use in
court for our DNA profiles. We included references which support our statement
as well as the peak heights on electropherograms showed adequate DNA where the amel
X dropout should not have occurred (Figure 9). We also sequenced amel X
and the results are seen in Table 4. References 43-46 address the X Dropout.
We can address this exponentially if necessary.
9. More vagueness: how were the complete mtDNA genomes obtained? Apparently the samples were sent to a company, I guess they amplified it in overlapping fragments? of which length? Or were they captured with some enrichment method and posteriorly sequenced with next generation technologies? One cannot say the samples were sent and results sent back and that's it
9. More vagueness: how were the complete mtDNA genomes obtained? Apparently the samples were sent to a company, I guess they amplified it in overlapping fragments? of which length? Or were they captured with some enrichment method and posteriorly sequenced with next generation technologies? One cannot say the samples were sent and results sent back and that's it
Authors’ Response:
From
Materials and Methods: Aliquots of
purified DNA from all of the samples in this study, along with human controls
to monitor for possible contamination, were shipped to Family Tree DNA.
Proprietary methods were used to amplify the mitochondrial DNA genome. The DNA
was amplified using 48 sets of human specific primer pairs that overlapped.
Extra primers were developed and utilized in case of failure due to mutation.
The amplicons were sequenced on an Applied Biosystems® 3130xl Genetic Analyzer.
10. Instead of generating meaningless mtDNA phylogenetic trees, the authors should check the well known mtDNA phylogeny (for instance, at PhyloTree) and tell us exactly the haplogroup, and/or subhaplogroup and haplotypes of each sample. It will be self evident anyway that these mtDNA genomes fell within the modern human variation, no need for any tree.
Authors’ Response:
We were asked for the mtDNA
phylogenetic trees in the first submission so we furnished them. They
were actually important since the same mtDNA sequences were found in the next
generation whole genome sequencing as in the original mtDNA sequencing.
We furnished trees for both the original individual mtDNA sequencing as well as
the sequence pulled from the whole genomes. We furnished a table with
haplogroups for the various samples (Table2).
11. Unsupported claims (by the way, allelic dropout is a well known phenomena in degraded samples and still the most plausible explanation): "It is noteworthy that AmelX allele dropout occurs in significant numbers of the unknown samples yet seldom occurs in normal human testing."
11. Unsupported claims (by the way, allelic dropout is a well known phenomena in degraded samples and still the most plausible explanation): "It is noteworthy that AmelX allele dropout occurs in significant numbers of the unknown samples yet seldom occurs in normal human testing."
Authors’ Response:
We have previously addressed that
the samples were not degraded. We also furnished
references for the X dropout (References 43-46) and the peak height (RFU) of
the Y peak precludes degraded or insufficient DNA as a cause of X dropout (Figure 9). The samples were
tested twice with different methods (PP16 and amelogenin only) and the dropout
repeated. Amel X was also sequenced and it failed on most of the samples
though the human controls provided normal sequence. Three of the authors have seen literally
thousands of PP16 profiles from both paternity and forensic applications. Only one author has actually seen one case of
X dropout and it was because of mutation, not degradation or low yield
DNA. From the paper: The genotyping of
the amelogenin locus produced the most consistent results across the samples
tested. The DNA samples yielded four types of results: XX, XY, Y and null. The
dropout of the X amplicon was the most significant of the findings observed
with the STR genotype analysis of Amelogenin. (Figure 9, Supplementary Data 3)
This dropout was reproduced in several individual samples and was repeatable
both in the multiplex of PowerPlex 16 and the analysis of the STR locus, so it
is unlikely to be an experimental artifact due to low quantity or degraded DNA
(Table 3). The repeatability and number of samples exhibiting the X dropout is
inconsistent with what would be expected with normal human allele dropout43-46.
It is noteworthy that AmelX allele dropout occurs in significant
numbers of the unknown samples yet seldom occurs in normal human testing.
12. More vagueness (how long? how do
you assess pristiness?): "DNA samples that yielded long and pristine
sequences".
Authors’ Response:
The quality of the DNA sequences can
be assessed by viewing the electropherograms.
These are available if needed.
Also the Q30 score for the whole genomes denoted the extremely high
quality of the sequences, Lines 544-558.
13. More methodological problems (the observed -again, vague- results are likely due to the amplification of environmental and degraded DNA yielded unspecific PCR products):"The resulting sequences ranged from totally non homologous matches, not found in Genbankafter multiple BLASTs (including dissimilar sequence BLASTs) to novel SNPs and even failure to sequence"
Authors’ Response:
The quality of the DNA was addressed
using Figures 7 and 13 and the Q30 scores.
The novel sequences and SNPs repeated in the genomes although there was
no failure in the whole genomes.
Failures in the early testing can be attributed to primer design failing
to amplify novel sequence.
14. More methodological problems: the MC1R sequences (which primers?, which length?), come apparently from PCR products that were not cloned (this is an standard procedure while working on ancient DNA samples to ascertain the heterogeneities present in the PCR product and also the original extract). Thus the C to T change observed in two samples could be the result of cytosine deamination, a well known phenomenon in degraded DNA. In any case, what can be deduced from this section (and also from the mtDNA and the MYH16 section) is that this samples are modern human DNA samples.
Authors’ Response:
We have previously discounted
degradation of the DNA using visualization by yield gel and Q30 scores on the
next generation sequencing. Also, this
is fresh, contemporary DNA, not ancient DNA.
Sample 26 was worked up thoroughly including histopathology that showed
fresh tissue with no degradation or bacterial contamination. Since a whole genome was sequenced with fresh
tissue and still provided the same results as were obtained in the early
testing, the only conclusion is that the genome is novel and high quality. It is no different than any other genome
sequenced today with fresh tissue or blood.
We have added the primers as Supplemental Data 9.
15. Meaningless experiments and
sections (obviously the low performance in the SNP chip is due to low quality
DNA): "In an effort to mimic severely degraded DNA that could explain the
strikingly low SNP matches obtained, one of the human controls submitted along
with the unknown hominin samples comprised non sterile blood that was purposely
maintained at room temperature in a moist environment for 4 days in an effort
to maximize degradation of the sample. Upon visual inspection, hemolysis of the
sample had occurred and bacterial contamination, which often correlates with DNA
degradation, was seen. An acrylamide gel was loaded with the degraded human
sample to assess the degradation and was visualized with ethidium bromide.
Smearing was observed".
Authors’ Response:
If the DNA is degraded, it will
smear on a yield gel. Yield gels
have been used for years in forensics and standard DNA testing to assess DNA
quality from fresh specimens. We have figures of two yield gels showing DNA
that is not degraded and two samples that are showing some degradation,
including the human control, Figures 7 and 13.
16. More meaningless sections (artifactual or missing bands are common in ancient DNA, this has been known for about three decades now): "Some of the samples appeared to produce normal amplicons that resulted in bands consistent with the human controls. Other samples displayed clear bands that appeared to be of different sizes than those expected of normal human amplicons. Yet others had multiple bands. Still other samples failed to amplify at all."
16. More meaningless sections (artifactual or missing bands are common in ancient DNA, this has been known for about three decades now): "Some of the samples appeared to produce normal amplicons that resulted in bands consistent with the human controls. Other samples displayed clear bands that appeared to be of different sizes than those expected of normal human amplicons. Yet others had multiple bands. Still other samples failed to amplify at all."
Authors’ Response:
This is fresh DNA and fresh dried
DNA and the degradation issue has already been addressed. The same samples would sequence long pristine
(via electropherogram) sequences up to 900 bases at other loci consistent with
human as well as novel sequences hundreds of bases long.
17. More vagueness (which ones?): "and forensic techniques to ensure that there was no human contamination"
17. More vagueness (which ones?): "and forensic techniques to ensure that there was no human contamination"
Authors’ Response:
See Materials and methods: “Since the presence of normal human DNA contamination of submitted samples
was a primary concern throughout this study, all samples were thoroughly
cleaned in a manner consistent with forensic testing procedures. In order to
further rule out contamination from human personnel and lab workers, samples
from submitters and scientists working with the samples were collected for
comparison with the results obtained in the various DNA tests.
Hair samples
were then sorted into two groups for extraction at DNA Diagnostics. DNA from
those samples containing 5-50 or more single hair roots were selected and the
roots clipped into 1.5 mL microcentrifuge tubes. The hair roots were
thoroughly cleansed with water and ethanol prior to extraction to remove any
extraneous DNA.
Hair roots were
placed in microcentrifuge tubes for DNA extraction and ATL buffer (Qiagen) was
added. These samples were digested with proteinase K (PK, 20 mg/mL) and
dithiothreitol (DTT, 1.0 M) at 56°C overnight, followed by a three-step organic
extraction procedure using phenol:chloroform:isoamyl alcohol (25:24:1) with an
additional PCI extraction. This process was followed by a butanol wash and
buffer exchange/concentration into TE-4 buffer (10 mM Tris, 0.1mM
EDTA, pH 8.0) using Microcon®-100 ultrafiltration devices
(Millipore, Billerica, MA)92-93.
The remaining
unknown hairs with only 1-5 hair roots were sent to the North Louisiana
Criminalistics Laboratory (NLCL, Shreveport, Louisiana) for DNA extraction and
purification. The roots were cleaned with water prior to digestion. The cleaned
roots were digested in ATL buffer (Qiagen), PK, and DTT at 56°C until
completely dissolved, which generally was overnight. The DNA in this crude extract
was purified using the EZ1® DNA Investigator Kit with cRNA (Qiagen)
and eluted into TE-4 on a BioRobot EZ1® (Qiagen).
Saliva swabs, blood swabs, and tissue
cuttings (10 mg) were placed in microcentrifuge tubes for DNA extraction. The
samples were extracted using the above mentioned organic method with the
exception that DTT was not used during digestion.
Reference
samples, in the form of buccal swabs from submitters who collected the unknown
hair and tissue samples, were isolated using 50mM NaOH and heated to 100 for 10 minutes followed by the addition of 1M
Tris (pH 8.3)98. The DNA extracted at DNA Diagnostics was quantified
using a Nanodrop™ spectrophotometer (Thermo Scientific, Willimgton,
DE). Hair samples sent to the NLCL were quantified by real time PCR using the
Applied Biosystems Quantifiler® Human kit on an Applied Biosystems
Prism® 7000 Sequence Detection System99. Samples that yielded DNA concentrations too
low to use in standard testing had their DNA concentration augmented using multiple
displacement amplification method per the manufacturer’s instructions86.
DNA was then
visualized on a 1% agarose gel to determine DNA quality by loading 3 µL of DNA
extraction. Appearance of the bands
determined the quality and quantity of the DNA extraction (Figures 7 and 9)”.
18. More vagueness: "According to the laboratory, the sequences themselves
were of very high quality"
Authors’ Response:
We have added information and the
summary generated by the HiSeq 2000 Next Generation Sequencer showing that the
genomes were of high quality via the Q30 score, Lines 478-492, and removed the
statement above since it is no longer necessary due to the generated Q30
scores.
19. More methological problems (environmental, contaminating DNA will produce no matches at GenBank, this is common in all ancient DNA genomic projects): "Some sequences produced no homology matches when BLAST searched against all primate, human, Neanderthal, Denisova, and other sequences in Genbank."
Authors’ Response:
We previously addressed that 1. The
DNA is not ancient and 2. The DNA was not degraded or contaminated both by
visualization and testing in the case of preliminary findings and by the Q30
scores generated by the HiSeq2000 for the whole genomes.
20. Although they claim to have generated 30x genoms, I understand they have only assembled and analyzed the chromosome 11, they don't explain why.
Authors’ Response:
We explained that chromosome 11
is highly conserved in primates. In the paper: “Thus, the selective
supercontigs comprised an abundance of neural associated and putative tumor
suppressor sequences all of which are highly conserved in primates and humans
and clearly establish that the Sasquatch is closely related to humans. The high
homology with multiple primate lineages (including but not limited to,
chimpanzee, macaques, gibbons and marmosets) and with humans as demonstrated in
phylogenetic trees (Figures 19, 20, and 21) indicate that the supercontigs
contain highly conserved human and primate gene sequences”.
The goal of this manuscript was to
prove that there exists an unknown primate living in North America since
eyewitness reports consistently describe a creature with the appearance of a
primate. It takes years to analyze a
genome so in order to prove that we had a novel primate, it stood to reason
that an area of the genome that is highly conserved in primates be the first
area of the genome to be investigated.
The supercontigs supported the existence of a novel primate using
chromosome 11, which was the goal of this manuscript.
21. The obvious explaination for this section is that the sample is a mixture of DNAs or has been contaminated at the Sequencing Service (did they use a tag sequence for this particular project?; was the service sequencing primates?): "the Sasquatch consensus sequence that showed homology to human chromosome 11 reference sequence is distantly related to multiple primate lineages including Homo Sapiens, Pan Troglodytes (Chimpanzee), Macaca Mulatta (Rhesus Monkey), Nomascus Leukogenys (White cheeked Gibbon) and Callithrix Jacchus (Common Marmoset)."
21. The obvious explaination for this section is that the sample is a mixture of DNAs or has been contaminated at the Sequencing Service (did they use a tag sequence for this particular project?; was the service sequencing primates?): "the Sasquatch consensus sequence that showed homology to human chromosome 11 reference sequence is distantly related to multiple primate lineages including Homo Sapiens, Pan Troglodytes (Chimpanzee), Macaca Mulatta (Rhesus Monkey), Nomascus Leukogenys (White cheeked Gibbon) and Callithrix Jacchus (Common Marmoset)."
Authors’ Response:
The UT core lab only sequences human DNA and
this statement has been added on Lines 472-473.
We also previously addressed that we have added the Q30 scores for the
genomes. These scores absolutely prove
that there was not a mixture of species in the whole genomes as explained
above. Lines 544-558 from the manuscript: The run summary
generated by the HiSeq 2000 next generation sequencer provides scores, Q30, for
run quality. Q30 can also be used to determine if there was any contamination
(or mixture) found in the samples sequenced.
According to Illumina, a pure, single source sample would have an
average Q30 score of 85. However, if there was contamination present in the
sample sequenced, the divergent sequences would compete against one another
causing a contaminated sample to have a Q30 score of 40 to 50. The Q30 scores for the first read for the
three genomes sequenced had Q30 scores of 92, 88 and 89 respectively. The second read was slightly lower 88, 84.25
and 83.66, but still in line with the 85 average. The Q30 is the percent of the
reads that have the statistical probability greater than 1:1000 of being
correctly sequenced. Therefore, not only were the sequences from a single
source, but the quality of the sequences were far above the average genome
sequenced using the Illumina next generation sequencing platform. The high
quality of the genomes can be attributed to the stringent extraction procedures
utilized whereby the DNA was repeatedly purified. This ultra-purified DNA also allowed for
greater than 30X coverage of the three genomes.
The summary of the next generation sequencing generated by the HiSeq
2000 Illumina sequencer is furnished as Supplementary Data 7.
22.
Sequencing data should be freely available to the scientific community after
publishing (even better, before).
Authors’ Response:
We attempted to upload all sequences
to GenBank but they refused them (I have the email and it said because we do
not have a species name). We asked how to do it and they refused to
return our emails or calls). As a result, we attached all sequences as supplemental
per Dr. Gee's request.
23. In my view, there conclusions
are not supported by the data. What do we have here is likely low quality DNA samples
belonging to modern humans that yield some conflicting results in unspecific
genotyping approaches. I suggest also some background contamination in the next
generation sequencing from previous primate sequencing projects, again likely
influenced by the original low quality of the samples.
Authors’ Response:
This is an incorrect assumption as
the data was repeatable and of good quality.
We have defended our position numerous times (above) and have added new
data (Q30 scores) supporting our position that the DNA is not degraded nor is
it contaminated.
Referee #3 (Remarks to the Author):
I appreciate the additional work the authors have undertaking trying to meet the concerns raised by me and the other reviewers. However, I am afraid that I do not find the paper worth publishing. The authors still lack explaining in any convincing way how this "new species" carries mtDNA genomes identical to those of modern humans only. I also believe that alternative explanations exist as to why the nuDNA genomes differs from that of contemporary humans e.g. mapping a mixture of animal DNA and human contamination to human reference genomes.
I appreciate the additional work the authors have undertaking trying to meet the concerns raised by me and the other reviewers. However, I am afraid that I do not find the paper worth publishing. The authors still lack explaining in any convincing way how this "new species" carries mtDNA genomes identical to those of modern humans only. I also believe that alternative explanations exist as to why the nuDNA genomes differs from that of contemporary humans e.g. mapping a mixture of animal DNA and human contamination to human reference genomes.
Authors’ Response:
We felt that the data should speak
for itself so we did not include a theory concerning the lack of novel SNPs in
the mtDNA or the presence of the modern human mitochondrial DNA across all 110
samples. We have added a theory to the
Conclusions Section in the manuscript, Lines 734-738.
We
also previously addressed that we have added the Q30 scores for the
genomes. These scores absolutely prove
that there was not a mixture of species in the whole genomes as explained above.
Lines 544-558 from the manuscript: The run summary
generated by the HiSeq 2000 next generation sequencer provides scores, Q30, for
run quality. Q30 can also be used to determine if there was any contamination
(or mixture) found in the samples sequenced.
According to Illumina, a pure, single source sample would have an
average Q30 score of 85. However, if there was contamination present in the
sample sequenced, the divergent sequences would compete against one another
causing a contaminated sample to have a Q30 score of 40 to 50. The Q30 scores for the first read for the
three genomes sequenced had Q30 scores of 92, 88 and 89 respectively. The second read was slightly lower 88, 84.25
and 83.66, but still in line with the 85 average. The Q30 is the percent of the
reads that have the statistical probability greater than 1:1000 of being
correctly sequenced. Therefore, not only were the sequences from a single
source, but the quality of the sequences were far above the average genome
sequenced using the Illumina next generation sequencing platform. The high
quality of the genomes can be attributed to the stringent extraction procedures
utilized whereby the DNA was repeatedly purified. This ultra-purified DNA also allowed for
greater than 30X coverage of the three genomes.
The summary of the next generation sequencing generated by the HiSeq
2000 Illumina sequencer is furnished as Supplementary Data 7.
I want to thank the anonymous source for having the courage to come forward and give us vital information about the Ketchum DNA Study. It is my desire that this information will help those in the Bigfoot Community and the general public at large to understand the study and the events that have occurred over the past nine months.
This comment has been removed by a blog administrator.
ReplyDeleteI know exactly what this means Scott. Do not stray. The data in this review was only slightly questioned; alas, the grammar was actually requested to change more than. With the majority of Q30 scores contained in this ms, the data is not mostly erroneous, but rather correct. Most have no idea what CH11 is or what it does. Nor do they know what amel x allele is either. Carry on accordingly.
ReplyDeleteOn the battlefield; stall, delay and harrass tactics
ReplyDeleteserve to give advantage to a superior force that has not
yet arrived. Superior or not the one wanted to win. This
could happen in science, could it?
hopefully skyes will have simular findings as this study,
ReplyDeleteat this point, with all the negative press, it's the only thing that is going to redeem it.
A bit confused here. Ketchum admitted on her site that she DID NOT pass peer review.
ReplyDeletehttp://www.advancedsciencefoundation.org/#!press-release/cm8a
Are the above just made up lies? What's going on Scott?
Ed, please stop lying and trying to confuse the reader, I checked this link of her so called "Journal". Dr. Ketchum did not set this up nor did she make an entry. The "admission" you are referring too is a statement made by "Melba's friends, family, and closest loved ones... "
DeleteBelow is the actual quote. If you cannot be more honest in the future I will have to block you from commenting. I do not mind you stating your opinion, but when you purposely attempt to mislead (LIE) then I will have to draw the line. Ed, you have been warned, do it again and your banned.
Here is the quote:
As Melba's friends, family, and closest loved ones... it became our intent to facilitate and establish an online platform where Melba could freely self-publish her ground breaking science. Her work and manuscript were rejected by NATURE in November of 2012, then rejected again by JAMEZ in January 2013, and promptly rejected again by another scientific online journal toward the end of January / beginning of February 2013. All of these three American Journals as well as the International Journals who rejected Melba should be boycotted for their blanted scientific bias against Melba and her work. She is a brilliant scientist, self-taught geneticist, and loving veterinarian.