Monday, March 18, 2013

Calling on Dr. Ketchum to Retract Her Sasquatch Paper

That's my opinion.  If Dr. Melba Ketchum thinks there is serious research to be done in the field of sasquatch, and that there may actually be an unknown North American primate, then she needs to improve the credibility of the field by accepting that something, somehow, went very wrong in her efforts, and make a retraction.

Consider two recent DNA stories, both announced outside the peer-reviewed journal system. (While I understand Dr. Ketchum's frustration with the exhausting process of scientific publication,  her never-published, self-owned journal, carrying nothing but her own paper, does not impress.)

The other recent DNA-related story was the announcement, based on work carried out mainly by volunteer  enthusiasts and announced in the press vs. a journal, on the finding of Richard III's remains.  There are both similarities and differences in the two cases.

On the "difference" side, the announcement by Richard III researchers produced data that appeared reasonable on its face (that is, it matched with historical accounts and the appearance of the remains well enough to be plausible). It was an interesting finding, but, if true, would be nothing radical, whereas Ketchum's work (as well she knew) was going to be a major challenge to orthodoxy and thus needed to be near-flawless.
Similarities: the Richard III work has NOT been universally accepted, as other scientists cautioned about contamination and noted that matching mitochondrial DNA does not narrow the remains down to a particular individual or even, with certainty, a family. So the data and interpretations were critiqued along with the method of publication.
Dr. Ketchum's analysis of her own data initially indicated an evolutionarily implausible scenario, involving an ancestor related to no known primate that seemingly appeared one time and then disappeared. I've seen one outside scientist who thought it deserved examination vs. many who thought it absurd. Then came news that the unknown ancestor was related to lemurs, which moved her theory from implausible to impossible.  No trace of lemurs exists in the New World or anywhere closer than Africa, and the finding guarantees no one will take her case seriously as anything but the results of contamination, despite her protests that all precautions were taken. A human and a large lemur-related primate are from different suborders, let alone families or genera. They have the same chance of producing a baby that a dog and a cat would - none whatsoever. She told an interviewer that the result doesn't fit with Darwin's theory of evolution.  That's correct, and that means it will not be supported by any qualified scientist. (There's a huge difference between arguing we have the details of primate evolution wrong and arguing the entire concept of Darwinian evolution and the present concept of DNA development must be thrown out.)

I wanted Dr. Ketchum to be right. I think she is sincere, but right? I don't believe there is any chance that she is, and the scorn of outside scientists has convincing reasoning behind it, even if some of the language is intemperate.

Thanks to Terry Colvin for the email post that raised the question of comparing the two events.
Another piece of the puzzle here.


lark said...

I think you are running with some things Melba Ketchum said, unfairly to her.
I read her paper. Actually her hybrid findings seemed to me to rationalize things that have been mysterious about the sasquatch phenomenon, which you would hope the truth would do.
She didn't say in the paper that sasquatches were a human-lemur hybrid, but rather human with unknown hominin hybrid.
The lemur part seems to have come from her attempt to look for homology of the sasquatch nuclear DNA with primate nuclear DNA sequences. Fig. 16 in her paper suggests that the sasquatch nuclear DNA sequences are close to "Otolemur garnetti". It doesn't mean that sasquatches are a human-lemur hybrid, that would be silly.
The last part of her paper, trying to analyze the sasquatch nuclear DNA sequences, seems tacked on and badly done. Leonid Kruglyak complained that Fig. 16 made no sense, and if a geneticist is puzzled, it needs to be much better explained.
I think Melba Ketchum is outside her area of expertise in attempting this computerized analysis of the DNA sequences.
It doesn't mean that the main part of her work - gathering sasquatch samples, cleaning them, sequencing them - is bad.
MK said the quality scores for the sequences were very high. This was next-generation sequencing, using human DNA as a scaffold. She said if there was contamination, the contaminating sequences should be competing with the unknown (sasquatch) DNA, lowering the quality score.
However, how much sequence data did she actually get? MK says in the paper
"The DNA from these three samples was sequenced using the next generation Illumina platform at the University of Texas, Southwestern in Dallas, TX, a laboratory that sequences human genomes​. On average, there were 70-110 million total reads for each sample in each lane, which is well over 90 Gb of raw sequence for each sample comprising greater than 30X coverage."
The human genome has about 3 billion base pairs, so MK is saying she sequenced the entire sasquatch genome.
So if there were contamination, it should have competed with the sasquatch DNA.
Perhaps sequencing the sasquatch DNA samples using human DNA sequences as a scaffolding, isn't a good idea and messed up the analysis. Maybe the sasquatch DNA needed to be sequenced as a novel DNA sequence, which is more expensive (they have a limited amount of money).
MK distributed about 5 million base pairs on chromosome 11 with her paper, but where's the rest of the genome? Is there more work involved in coming up with a consensus between the 3 samples she used for nuclear DNA?
Sasquatches as human/hominin hybrids seems reasonable to me because:
- a hybrid could lose human abilities like tool-making and fire-making. Hybrids are often dysfunctional to some extent.
- a hybrid could be larger than either of the parents, because hybridizing can change how growth is regulated. There's a lion/tiger hybrid that is larger than either a lion or a tiger, for example.
- however the hybrid could have enough of human intelligence, and be similar enough to humans, to avoid leaving obvious signs of their presence around; avoid being hit by cars on roads - so they wouldn't be seen.
- sasquatches seem to be about 7-8 feet tall in the more credible reports - this is a height that might work in a hybrid. When people report 12' tall sasquatches, maybe they're overestimating the height because they're scared.
- humans have hybridized with other hominins throughout our evolution - not only with Neanderthals, but at least according to an article I read, we have other human relatives in our genes as well.
- why would it be surprising that the hominin ancestor of sasquatches, hasn't left a fossil record? why would anyone think that the fossil record of hominins is complete, when new hominins are still being discovered?

Matt Bille said...

Lark, thanks for taking the time to comment in such depth. I'll post a response as soon as I have time to give it proper attention.

Matt Bille said...

Lark, to give it a little more thought...
First, I'm not qualified to critique the DNA findings themselves. However, Dr. Ketchum raised the similarity, as you said, at one point to a lemur species. She went on to day: "It's headed a little more towards the lemur line, oddly enough. It is definitely NOT an ape. And it's interesting that we found out that there is an extinct lemur that weighed 400 or 500 pounds. Also, they had opposable thumbs and hooded noses. It really freaked me out that we had lemur. I did not expect that (laughs)."

I will grant that Ketchum did NOT say directly that she thought a lemur was half the hybrid species. But there simply isn't a sequence of events that allows DNA strongly convergent to a lemur to appear in a human or half-human being. And, while not being a DNA expert, I will note that everyone who is says the paper was bad. Paleobiologist Dr. Darren Naish is not closed-minded - he believes in some mammalian form of "sea serpent" - but when he reviewed her paper for a journal he found it sloppy and unconvincing. I'm the first to stipulate that Dr. Ketchum is sincere and thought she and the labs she contacted were handing everything very carefully. But if the response comes out as what geneticists have said in the media is nonsensical or impossible, something went wrong.
Your thoughts on a hybrid are worht noting. Yes, a hybrid can be bigger than its parents, though not enormously bigger except in freakish circumstances (since the liger is the only example I can come up with). Given that the choice of human ancestors here are all smaller than modern humans, it seems to me Denisovians or Neanderthals aren't going to produce this giant, and H. erectus, as far as we know, never made it remotely close to areas where it could have used sea or land bridges (and it and the australopithecines were also smaller, even the branch that used to be called Paranthropus robustus). Gigantopithecus was, I think we've established quite clearly, an ape too far from the human tree. You are right that we don't have all the human-related species located: I think there more fossil remains will be found. If we do find anything that might, genetially, physically, and right in space and time, could have been the source of a hybrid, and might have had a bit of DNA similar to lemurs, I would re-evaluate my opinion.
I don't think I'm being utra-skeptical here. I think some mystery apes, notably orang-pendek, exist: sasquatch is unlikely but not impossible. I just don't think the science has been advanced by Dr. Ketchum's efforts here, and it would be better to take a step back. The Oxford DNA project is much more likely to produce sceintifically convincing results.