Guest Posted March 11, 2013 Share Posted March 11, 2013 (edited) Doesn't the illumina platform have several different modes it uses in the assembly of the sequences? 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 Edited March 11, 2013 by ridgerunner Link to comment Share on other sites More sharing options...
Guest njjohn Posted March 11, 2013 Share Posted March 11, 2013 Well I've heard the 1% data was actually not data, so I guess that negates any independent analysis at this point. It was the contigs which can be directly blasted. It's basically the un-raw data. It could have easily been (but time-consumingly annoying) just typed out randomly. I don't think that's what happened, but it's possible. It allows the DNA sequences in those contigs to be analyzed. That analysis hasn't come close to proving the claims of the paper. The poster that asked for a peer-reviewed study refuting her claims... they're all waiting. They need the full raw data in order to see what they have to refute. If I told you I'm typing this out on a pink keyboard. My only proof that I supplied were pictures of the keys that I had removed from said keyboard, but they're black with white lettering. Two other posters searched through every keyboard database known and came back with a grey keyboard both times. I then come out and say, well prove my keyboard isn't pink. It's something that can't be proven. Just like her report can't be completely refuted without her released raw data. I don't know if that's intentional or not, but it leads to doubt all around. But science doesn't rely on that. It can see if even that 1% makes sense in comparison to her claims and so far, every analysis has said no. Link to comment Share on other sites More sharing options...
chelefoot Posted March 11, 2013 Share Posted March 11, 2013 Time Out! This thread is way off topic. It will be closed while we deal with this. Link to comment Share on other sites More sharing options...
chelefoot Posted March 11, 2013 Share Posted March 11, 2013 We are discussing "The Ketchum Report". Please make sure your post is related to the topic before hitting the button! Thank you to everyone who have been discussing the topic. Have a wonderful evening! chelefoot Link to comment Share on other sites More sharing options...
Guest Tyler H Posted March 11, 2013 Share Posted March 11, 2013 Questions for you: Who are the people that "unanimously" repudiate her conclusions? Who is your qualified Phd? Surely you can suppport those 2 allegations of yours, correct? Thanks. Where o where have you been J Sasq? Have you not read any posts in this thread? I know of 4 people on this forum who claim to have advanced genetic or biology credentials: Genes R Us, Tomafoot, RidgeRunner and Theagenes. Tomafoot has been quiet for some time now, so I guess I can't state whatever his opinion is on this at present. But as for the other three, they have all repudiated Melba's data and conclusions. As I have siad many times now, my 'qualified PhD' who has contributed things like the .pdf (which is transparent data taken from Melba's report, and which efforts can be replicated by anyone) wishes to remain anonymous. But my posts by him have been "peer reiviewed" so to speak, by the credentialed people on this forum - they have supported each statement from him. I also have 3 other PhD's that I am in contact with, but whose comments I have NOT posted, because they did not give me permission to post their comments, even anonymously. ANd guess what - they too repudiate Melba's work. Now, you are going to say that you don't believe me, and that I can't prove who these people are, blah blah blah... that's fine. Don't believe me... but in the meantime, go out and get some statements from your own PhD's or some reputable, credentialed person who can comment on the data insightfully. You are not capable of that. (Not saying that I am either). All you are capable of is plugging your ears, closing your eyes and repeating over and over "I can't hear you" and "I know you are, but what am I?" - you won't accept anything, but you contribute no insightful critique, and no rebuttals to the specific charges levelled against this data. Refute the .pdf, and other specific concerns that have been raised by credentialed people, or pipe down. I think I'll just wait for Tyler to answer the questions put to him. He should be able to answer them correctly. Thanks for a valiant attempt at filling in for him though. He will understand the question. WHat the heck is the difference if Leisureclass lists 3 POhd's or I do, or whomever? If they are qualified people, they are qualified people - how does it change if I list 3, or he lists 3? All it does is double up the evidence against you - we now have my 3 (or 7, depending how you count them) and Leisure's 3... so that's at least 6... how many would you like to cry for, before you actually contribute ONE? Link to comment Share on other sites More sharing options...
Drew Posted March 11, 2013 Share Posted March 11, 2013 In order for any hybrid to exist as a separate group, there must be two factors: 1. The two parent species must be able to breed. 2. The offspring of the two parent species must then be isolated from both parent's species. From what I have read, neither one of the above seems plausible. Link to comment Share on other sites More sharing options...
Guest J Sasq Doe Posted March 11, 2013 Share Posted March 11, 2013 Where o where have you been J Sasq? Have you not read any posts in this thread? I have read this thread, but there has been precious little on the matter of Dr. Ketchum's study. A bunch of folks have gone all TMZ on Ketchum, and have muddied the waters a bit. they have all repudiated Melba's data and conclusions. Impossible to do without the data being released. Perhaps your interpretation of their postings is incorrect. As I have siad many times now, my 'qualified PhD' who has contributed things like the .pdf (which is transparent data taken from Melba's report, and which efforts can be replicated by anyone) wishes to remain anonymous. But my posts by him have been "peer reiviewed" so to speak, by the credentialed people on this forum - they have supported each statement from him. I also have 3 other PhD's that I am in contact with, but whose comments I have NOT posted, because they did not give me permission to post their comments, even anonymously. ANd guess what - they too repudiate Melba's work. Ah, well, so it's not just your neighbour Bob, with a dog-eared copy of DNA For Dummies. You have a cadre of top secret people researching this for you...but not willing to put their names on it. That tells you right there what it's worth. For the purposes of future identification in here, we can refer to them collectively as Dr. Vinny Boombatz. Now, you are going to say that you don't believe me, and that I can't prove who these people are, blah blah blah... that's fine. Don't believe me... but in the meantime, go out and get some statements from your own PhD's or some reputable, credentialed person I don't believe you. You have not supplied any factual basis for refuting any of Dr. Ketchum's claims in her study, yet you continue to wage your anti-Ketchum campaign. And now you have Dr. Vinny Boombatz in your corner. Wow, that'll impress 'em, for sure, eh? Refute the .pdf, and other specific concerns that have been raised by credentialed people, or pipe down. Put the name and credentials behind your pdf. Without that it's meaningless. WHat the heck is the difference if Leisureclass lists 3 POhd's or I do, or whomever? If they are qualified people, they are qualified people - how does it change if I list 3, or he lists 3? All it does is double up the evidence against you - we now have my 3 (or 7, depending how you count them) and Leisure's 3... so that's at least 6... how many would you like to cry for, before you actually contribute ONE? The questions were, who were the unanimous folks in here, and who was your Phd (Vinny Boombatz?), but leisureclass went off on a tangent and gave some names off the net. At least you read the question and understood it. That's what I was counting on. So anyways, who is your Dr. Vinny Boombatz? Link to comment Share on other sites More sharing options...
Drew Posted March 11, 2013 Share Posted March 11, 2013 Put the name and credentials behind your pdf. Without that it's meaningless. No. It is meaningful. We don't need the alleged data to be released, they clearly have contaminated human DNA, and made a leap to label it as Bigfoot. Please don't give out anyone's identity, it is not necessary. Link to comment Share on other sites More sharing options...
Guest Posted March 11, 2013 Share Posted March 11, 2013 J Sasq Doe said: I have read this thread, but there has been precious little on the matter of Dr. Ketchum's study. Well, what about Dr. Ketchum's paper do you feel should be discussed - that hasn't been to date? We really can't discuss all the "beautiful science" because the most important part (the beautiful science a/k/a the raw data) she did not release in her paper. So, I guess people will discuss what they have available to them. But, if there is something you find relevant or interesting in the paper, that hasn't been discussed, by all means please bring it up. Link to comment Share on other sites More sharing options...
JDL Posted March 11, 2013 Share Posted March 11, 2013 Every few days now I just check the last page of this thread. Each time I do I feel like Crocodile Dundee turning on the TV in his New York hotel room. Link to comment Share on other sites More sharing options...
Guest thermalman Posted March 11, 2013 Share Posted March 11, 2013 (edited) @JsasqDoe, Secret references and "angel claims" remind me a lot about Kit's suit, non existent and fact less rhetoric. A mute, null and void discussion requiring no further interaction if the claimant continues to withhold his sources. It's that simple, so don't waste to much time with those who carry on with such "empty as a drum" allegations. Edited March 11, 2013 by thermalman Link to comment Share on other sites More sharing options...
Guest Posted March 11, 2013 Share Posted March 11, 2013 Thermalman - you can probably blame Ketchum for the "angel claims" - as she is the one who first brought up and used the word, "Angel". Also, Ketchum keeps referring back to this data that she didn't release in her paper - talk about a secret reference.. No one knows what that raw data looks like, but Melba. Who are these, "scientists whose names we would all know if she said them," that she said stepped forward to help her, once her paper was released? Are they still working with her? Have they come up with anything? Talk about secret. Did you ask her if she will be releasing the raw data in her paper? If she won't could you find out why? That raw data seems to be very important. Link to comment Share on other sites More sharing options...
Guest Posted March 11, 2013 Share Posted March 11, 2013 Impossible to do without the data being released. Would you agree that Dr. Ketchum's claims are impossible as well as she hasn't included any of that data in her paper? Link to comment Share on other sites More sharing options...
Guest Posted March 11, 2013 Share Posted March 11, 2013 (edited) Thermalman - you can probably blame Ketchum for the "angel claims" - as she is the one who first brought up and used the word, "Angel". Also, Ketchum keeps referring back to this data that she didn't release in her paper - talk about a secret reference.. No one knows what that raw data looks like, but Melba. Who are these, "scientists whose names we would all know if she said them," that she said stepped forward to help her, once her paper was released? Are they still working with her? Have they come up with anything? Talk about secret. Did you ask her if she will be releasing the raw data in her paper? If she won't could you find out why? That raw data seems to be very important. There is no excuse IMO anymore for not communicating at least the status of the professed post pub review or GenBank upload.... I guess arrogance or dishonesty might explain the silence...or denial, or delusion....none are pleasing reasons. Oh! A lawsuit threat might be a reason for silence....did anyone notice that "Scholastic contacted by law firm" comment I posted from that OTLS! blog...? If there is a suit in the background or threat of...that would affect what is being said publicly now... And the records of Scholastic would reveal the ownership of FAZE/JAMEZ, etc...and go to the core of claimed per-review....so I can imagine a scenario/contract in which peer-review was the basis of the deal.....humm, interesting. or not! depressing actually. Edited March 11, 2013 by apehuman Link to comment Share on other sites More sharing options...
Guest Posted March 11, 2013 Share Posted March 11, 2013 there could be many reasons why she didn't release the data,but only assumptions can be made, until she comments on her reasons. Link to comment Share on other sites More sharing options...
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