The Ketchum Report (Continued)

[Guest]

I think this community was rallying for Melba before the paper came out! But I can not rally behind science and conclusions that I totally feel are false and misleading. In the end, blindly following a falsehood is not a good thing. Bigfoot is a biological creature, not a religion to have faith in.

[Guest]

ridgerunner said:

Bigfoot is a biological creature, not a religion to have faith in.

Absolutely and I could not agree more.

If we want the world to take us seriously - we should take what we do seriously.

Edited to add:

So, has the scientific community stopped talking about this paper? I haven't seen or heard anything recently... So, I am gonna assume it's over as far as their concerned.

Edited March 11, 2013 by Melissa

[Guest Tyler H]

I understand TM, just trying to keep this on track.

Thanks,

KB

thanks kb

[Guest]

So, has the scientific community stopped talking about this paper? I haven't seen or heard anything recently... So, I am gonna assume it's over as far as their concerned.

I think that's an accurate assumption.

[Guest]

@Melissa,

Science had a small mention of her pre-publication (post-Russian-leak) press release

Random Sample, Science, 30 November 2012:1133-1134

but no mention after publication. I have not seen anything in Nature either, but if rumors are true, they were already familiar with the manuscript. So almost a month on, I think any further press on this is unlikely.

Edited March 11, 2013 by ridgerunner

[Guest]

There will never be a rally, most have there own agenda,rather see someone fail miserably, push them down, and destroy them any way they can, just like a scary character in a movie. The only way they will help is if there is something in it for them.

This study, with out a doubt, proved that

Edited March 11, 2013 by zigoapex

[Guest Tyler H]

"There will never be a rally, most have there own agenda,rather control all the information, take in huge amounts of money, hog the lime-light, try to become rich and famous, like a scary character in a movie. The only way they will help is if there is something in it for them.

This study, with out a doubt, proved that"

Edited March 11, 2013 by Tyler H

[Guest]

should of just added it in.

[Guest]

Thank you Leisureclass and Ridgerunner..

Well - this was ------ what's the word I'm looking for??? I would like to say unexpected - but many called this outcome long before this paper was published.

OHHH I know the word -- disappointed. But, as a bigfooter - I am getting used to that. I would love to throw a big ole LOL in here somewhere - but it's really not funny.

[Guest]

Melissa- I feel your disappointment also. It has been almost 54 years since I had my two ear encounters. About half of my family has had visuals very close and I missed my chance unknowingly settling for an ear encounter. I had been on a quest since up until recently and its left an anti-climax void in my life. So I keep telling myself to just stay the course and contribute where you can. I also have a feeling that due to modern tech that we inch closer every year to getting a picture of our quest. Let me just say that you are a cog in that wheel and not only do I read all your posts but enjoy them all. Hang in there gal, your a real trooper.

[southernyahoo]

There is a template or reference based assembly (like doing a jigsaw puzzle when you know that the picture is) and there is a de novo assembly, linking up the homologous ends of the sequencing reads using sophisticated computer algorithms (a jigsaw puzzle of an abstract painting that you don't know what it looks like - you have to match up each piece to see what fits). The Ketchum paper used human chromosome 11 as a reference.

What I don't understand is how, using the human chromosome 11 as a reference, the new sequence is so dissimilar to human chromosome 11. Perhaps the de novo approach would have lead to a better contig generation, but I feel there was a bias in doing the human reference due to the mtDNA results.

If the sequencing library was a mixed sample, various sequences from different species could be spliced together in the assembly process due to considerable homology between mammalian species. Because of the high Q30 scores, which we have already discussed, MK et al interpreted this to mean the sample was pure, even though this quality measure has no relevance to sample purity. A mixed sample would be much more difficult to sort out, and would have to be acknowledged as a mixed sample. In the MK case, they said their sample was pure, based in the Q30 score.

Tyler's pdf shows how a mixed sample could be assembled to have sequences form different species. The jigsaw pieces technically fit together, but the end assembled puzzle was a mixture of several pictures. Hope this helps

I found this in the materials and methods section.

Custom scripts were used

to extract reads showing good alignment to specific chromosomes of the reference genome.

Using CLC Bio Genomic Workbench version 5.1, the extracted reads were assembled to create a

consensus sequence using the targeted chromosome as a reference; also, de novo assembly using the extracted reads was performed to yield contigs. Both the assembled reads and the de novo

assembly contigs were fed to BLAST version 2.2.26 (blast.ncbi.nlm.hih.gov) with the following

settings: database Nucleotide collection (nr/nt), optimized for highly similar sequences

(megablast).

[Guest]

I found this in the materials and methods section.

Custom scripts were used

to extract reads showing good alignment to specific chromosomes of the reference genome.

Using CLC Bio Genomic Workbench version 5.1, the extracted reads were assembled to create a

consensus sequence using the targeted chromosome as a reference; also, de novo assembly using the extracted reads was performed to yield contigs. Both the assembled reads and the de novo

assembly contigs were fed to BLAST version 2.2.26 (blast.ncbi.nlm.hih.gov) with the following

settings: database Nucleotide collection (nr/nt), optimized for highly similar sequences

(megablast).

I saw that in the M&M, but it was not clear which procedure was used to generate the final sequence. Only one sequence is provided for each sample. Did you figure out what they did? I was not clear to me. And again, if they extracted sequences with good alignment to a specific chromosome, then assembled these sequences, why was the end product so far off from the reference sequence?

I was looking over some older posts and noticed one from you that I had a question for.

"The data that will really matter to me at this point is in the amelogenin locus and having to do with recombination in the X chromosome and a fully novel Y chromosome. If there is a consistency across the tested samples there , then there is evidence for what is proposed. If not, then I'll stick a fork in it myself."

I have not looked a this with too much detail, but from what I see, the results do not seem too consistent for either the genotyping (table 3) or the sequencing (table 4). Again, unfortunately, there is little sequence to analyze what was truly found. Do you have further thoughts on this?

[Guest]

I would also like to know the origin of the 1% claim.

As far as I can tell, the earliest reference to the "1%" was by Tyler in post #1256 - not clearly referenced prior to that. I might have missed an earlier post. I am guessing it is in response to the either the amount of sequence provided to the anticipated full genome (actually closer to 0.1%), or the amount of sequence provided in reference to Chromosome 11 (2%). Or I might be totally mistaken.

[southernyahoo]

According to Ketchum, the Amelogenin locus is quite Novel, as related to me prior to publication. Obviously if the male progenitor was not human "as we know it" the Y chromosome would be nearly pure gold, so to speak. The amel x dropout could theoreticly be because of the recombination levels. Just a guess. I do hope there is sequence there to analyse, as I don't think all those results are from the whole nuDNA genomes and include other samples.

[Guest]

Melissa- I feel your disappointment also. It has been almost 54 years since I had my two ear encounters. About half of my family has had visuals very close and I missed my chance unknowingly settling for an ear encounter. I had been on a quest since up until recently and its left an anti-climax void in my life. So I keep telling myself to just stay the course and contribute where you can. I also have a feeling that due to modern tech that we inch closer every year to getting a picture of our quest. Let me just say that you are a cog in that wheel and not only do I read all your posts but enjoy them all. Hang in there gal, your a real trooper.

No worries - I will put my head down and charge forward. It's what I do best. You are very sweet - and I thank you for the very kind words.