Sunday, September 15, 2013

Melba Is Toast: A Biochemist with a Ph.D. from Harvard Analyzes the Ketchum Bigfoot DNA Paper

Mid-September 2013 Edition

A longtime friend of mine, a tenured faculty member in biochemistry at a research university, with a Ph.D. from Harvard, has analyzed the Ketchum "Bigfoot DNA" paper, its techniques and methods, and its aftermath. Here is his statement:

"Melba Is Toast

The paper by Melba Ketchum and co-workers, published in an online journal Ketchum purchased just to publish her results, appears to be the product of careless work on impure samples and highly improbable conclusions. Here is a list of problems with the work. It is no doubt incomplete, but these are the obvious points.

1) The polymerase chain reaction (PCR) is a method for amplifying DNA. Ketchum and her team used it to obtain analyzable amounts of DNA from their samples. Since PCR amplifies DNA exponentially, any contaminating DNA can yield artifacts. This can reveal itself in products of unexpected size and sequence. The most likely interpretation of their observation of unusual products resulting from PCR of the samples is contamination. If one is not extremely careful with how one handles the source of the DNA samples, like hair, and the isolation of the DNA and all steps prior to PCR, then contamination is not just a possibility but a likelihood. Contaminating DNA can come merely from superficial contact, as it is on skin and hair. It could already be the sample (for instance, if the animal had killed and eaten another animal). It can originate from humans handling the samples or from any other organism whose DNA is present at any point, not only on site or during transport of the sample but also in any of the labs or facilities from any material that comes into contact with the sample (bench tops, improperly washed or autoclaved tubes or other lab implements, etc.) or even from bacteria on dust particles, which can be a problem if samples are exposed to the air for long. With regard to dust particles, much of the dust present in any normal setting under non-sterile conditions comes from human skin flakes (all people are constantly shedding very tiny flakes of skin, which contain not only human DNA but also microbes that feed on the skin). So there are myriad possible sources for contaminating DNA. One must be extremely careful to minimize such contamination in handling samples, especially for a very sensitive technique like PCR.

2) Other issues that can result in strange results are degraded DNA, as well as trivial but common things such as DNA polymerase enzyme that is no longer functional because of denaturation, forgetting to add a component of a reaction like the nucleoside triphosphate cocktail, not using the right buffer, etc. Experiments can fail and yield "false negatives" in addition to "false positives" or results that are "erroneous" in that they do not reflect what one thinks one is testing. This happens all the time. It is just the nature of experimentation, where there are many variables and many things that can go wrong, often without one ever knowing what went wrong. This is why it is so critical to be very careful with samples, perform the appropriate controls and repeat the experiments several times over (at least) to see if the results are repeatable.

3) Ketchum and co-workers found some European haplotypes from sequencing of their PCR products. They conclude, implausibly, that this is supported by the Solutrean hypothesis, an obscure idea that humans came over from Europe. The only basis for this hypothesis is that tools of the Solutrean culture, which existed in Europe between 17,000 and 20,000 years ago, seem to resemble tools from the Clovis culture, which developed in North America around 13,000 years ago. There are huge problems with this hypothesis - that Europeans came to North America around 13,000 years ago and spread tool-making to the mostly Asian-derived Native American population. Most archeaological and carbon-dating experiments emphatically do not support it. So why do Ketchum and co-workers jump to the most unlikely and assumption-laden conclusion to explain their data? Applying Occam's razor - that one should first go with and test the simplest of hypotheses when there are multiple explanations for something - would lead one to conclude that the sample was contaminated by one of the team members of European extraction.

4) In addition to the genotyping and sequence analysis, Ketchum and co-workers used electron microscopy to look at the DNA samples and found that some of the DNA would base pair with one complementary strand, but other parts would not base pair with anything at all and remain single stranded or base pair with another DNA molecule. Such DNA, if it originated from a single source, would be very strange. Even if they were, as they claim, looking at DNA from a hybrid of a female human and a non-human hominid male, the DNA would form double helical molecules. (A single or very small related source of maternal inheritance is concluded by Ketchum and her team since the mitochondrial DNA is human and seems to be from one source; mitochondrial DNA, unlike nuclear DNA, is inherited exclusively from the mother.) Ketchum and her team's assumption that their data support the notion of a single or very limited mating between a female human founder and a male non-human hominid is highly problematic, to say the least. First of all, the DNA would have undergone extensive DNA recombination since the time that the human and non-human hominid mated. Secondly, for successful mating to occur, the non-human hominid would have to be very closely related to humans. In that case, the DNA, even the non-coding regions, would be very similar and hybridization between the two would occur with nucleotide mismatches not going for long stretches of DNA for any given length of DNA; mismatching resulting in looped-out single strands would therefore not be observable by electron microscopy. Thirdly, even if the mating was between a human and a relatively distantly related non-human hominid (so that there was more extensive base mismatching) and was a relatively recent mating (so that much recombination would not have occurred yet), the two complementary strands of DNA from each chromosome from both the human and non-hominid ancestor would base pair with its own perfect complement rather than the other molecule (since that would be the most stable base-pairing pattern).

5) To reiterate and add to some points above related to the way their conclusions were an implausible stretch of the imagination, only relatively related species can mate and have fertile offspring. So the DNA should be very closely related one to the other. Even if they were more distantly related and bore fertile offspring, the sequences would be highly similar due to DNA recombination (and after 13,000 years or many hundreds of generations, there would be extensive recombination). Another weird assumption they make is that, while the hybridization resulted in fertile offspring, the offspring then did not mate with other pure humans or pure non-human hominid. Why did the hybridization occur only once or a limited number of times at the same period and place? Why was the hybridization confined to a human female and male non-human hominid? Why not a female non-human hominid and male human also (which is ruled out, even in their strange paradigm, by their not seeing non-human mitochondrial DNA)? How was an initial population big enough to support a breeding population generated? Obviously, there would have to have then been a lot of inbreeding, but how were enough even generated from a limited hybridization to lead to a non-out-breeding Sasquatch lineage from 13,000 years ago to the present? If the non-human hominid could breed with a human, why did it only breed with a supposed European-derived human in America 13,000 years ago and not also with Asian-derived humans, who obviously came over the ice bridge from Siberia to establish the Native American genome (by the way, there is no evidence of the presumed European ancestor in the Native American genome at all)? Also, why would all of the hybrids go off, live an isolated existence and not leave tangible evidence of this existence? What happened to the presumed non-human hominid that was the male founder of the Sasquatch lineage? It went extinct without leaving any archaeological or anthropological evidence of its existence? One could go on. It's all so very unlikely. It's a house of cards made of one flimsy card after another. It defies all evidence, any logic and is the product of pure faith.

6) A more minor point is that the Ketchum paper contains mistakes in interpretation or representation of the published literature. This reflects poor scholarship. In addition, there are many typos in Ketchum's response to the reviewers that was leaked. While this in and of itself does not necessarily mean that their handling of the samples or conclusions was sloppy (the above points do), it does show that they can be hasty, not pay attention to details and make statements without thinking too deeply about them. It is only human to view someone who is sloppy about a lot of little things as sloppy in big ways too, and it is often a correct conclusion.

It appears almost certain that the team was dealing with mixed samples of DNA, including contamination from team members or other people who may have handled the samples, and that they grasped at the least plausible answers to their results over and over again. They wanted to prove the existence of Sasquatch. Moreover, they were willing to go to very strange "places" in their interpretation of data that again and again most likely reflected contaminated DNA samples. They kept looking at the data and saying how can this prove that Sasquatch exists, reaching the least likely conclusions to support a more and more outlandish Sasquatch. This creature is as unlikely as the proverbial little green men."