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Antievolution.org Discussion Board > From the Panda's Thumb > After the Bar Closes... > Evolution of the horse; a problem for Darwinism?

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swbarnes2 Posts: 78 Joined: Mar. 2006 (Permalink) Posted: Oct. 16 2007,19:29    Quote I made a specific prediction.  Why do you want me to modify it to fit your scenario? If your hypothesis is to be of any value, it has to be applicable to more than just one organism and one survival challange, surely you see that. So, 50 labs, 5 post-docs and techs a piece, selecting for resistance to a particular antibiotic, for 3 months. Do you predict that all the resistant strains found will carry the exact same resistance-granting mutation?

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 16 2007,21:44    Quote (Daniel Smith @ Oct. 16 2007,18:44)     Quote (JAM @ Oct. 16 2007,15:07) What does your hypothesis predict if a different bacterial species is selected on nylon? I've already made my prediction, why are asking me to make another one? Because this has already been done!   Quote Quote 1) Will multiple selections give the same result, and/or 2) Will the enzymes that evolved be the orthologs of the ones that evolved in Achromobacter? My prediction was that exactly the same frame shift will occur - so I'm guessing it will be #1. Wrong! Completely different, nonhomologous gene. Would you like to see the data?             Quote   Quote P.S. Did you check out the mouse vs. rat sequences yet? I've been there several times.  Let me give you a blow by blow of my most recent visit: I want to see the mouse and rat genomes side by side so I go to VISTA and select the Mouse Feb. 2006 genome as a base genome, then I figure the best place to start is at the beginning,... Probably not. There are repeats, called telomeres, at the ends.       Quote so I select ch1:1-1000000 and click GO, I get an error saying "No such contig. or chromosome".  This is a bit confusing.  How can the mouse genome not have a chromosome 1? There's probably no contig for that region. The repeats make it complicated.       Quote So then I select ch2:1-1000000 and get the same error. Ch3 and 4 give the same results. So then I decided to try the Rat June 2003 and go with the default chr10:10000001-10100000, which then gives me some results. Yes, because you're in the middle, away from the junk at the ends that you thought would be conserved.       Quote I click on Browse alignment so I can see the coding (the Cs, As, Ts, and Gs).  I zoom in on a spot and when I put my mouse over the Rat code, it gives the number 10034062, when I cursor over the Mouse genome in the same spot, it gives the number 5312532.  I'm assuming these are the numbers for the position of that site within the chromosome. Correct, but it's not the same chromosome number. Why do you think that I tried to explain synteny to you?       Quote So, (if that's the case) it's not showing me the Rat and Mouse genomes, side by side - starting at position 10000001 and ending at position 10100000.  If it was, they'd both give the number 10034062 - wouldn't they? No, because contra your hypothesis, they aren't colinear. The autosomes are numbered according to their length, not their content. In fact, the place in which you were looking on rat chr10 has been inverted, and lines up with a bit of mouse chromosome 16, as VISTA tells you. These relationships are illustrated here: http://www.softberry.com/synt_pl....chr_2=* and in a different way, as well as conversely, here: http://www.informatics.jax.org/reports/homologymap/mouse_rat.shtml       Quote So, like I said, I'm not sure what I'm looking at and I'm not sure the correct way to use the site, but it doesn't appear to be giving me what I was looking for. Since your hypothesis is incorrect, what you're looking for doesn't exist. Rat chromosome 10 doesn't align with mouse chromosome 1, it aligns with chunks of mouse chromosomes 16, 17, and 11. Those represent translocations and inversions from the past. Therefore, none of those breakpoints have been conserved, and your hypothesis is incorrect. But all you had to do was look at the graph to see that between rat and mouse, there are big regions of no conservation between the pink lumps that are 80-100% conserved.     Quote So, if you have something you want me to see, you'll have to specifically tell me what it is I'm looking at and how it reflects on my hypothesis. Why are there gaps between the pink lumps that are the conserved sequences when we align orthologous sequences from two species within the same lineage?

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 17 2007,18:31    Quote (JAM @ Oct. 16 2007,21:44)     Quote (Daniel Smith @ Oct. 16 2007,18:44) My prediction was that exactly the same frame shift will occur - so I'm guessing it will be #1. Wrong! Completely different, nonhomologous gene. Would you like to see the data? Yes, I would be interested in seeing that.       Quote                 Quote       Quote P.S. Did you check out the mouse vs. rat sequences yet? I've been there several times.  Let me give you a blow by blow of my most recent visit: I want to see the mouse and rat genomes side by side so I go to VISTA and select the Mouse Feb. 2006 genome as a base genome, then I figure the best place to start is at the beginning,... Probably not. There are repeats, called telomeres, at the ends. I'd like to see those - just for my own curiosity.       Quote             Quote so I select ch1:1-1000000 and click GO, I get an error saying "No such contig. or chromosome".  This is a bit confusing.  How can the mouse genome not have a chromosome 1? There's probably no contig for that region. The repeats make it complicated. What is "contig"?       Quote             Quote So then I select ch2:1-1000000 and get the same error. Ch3 and 4 give the same results. So then I decided to try the Rat June 2003 and go with the default chr10:10000001-10100000, which then gives me some results. Yes, because you're in the middle, away from the junk at the ends that you thought would be conserved.           Quote I click on Browse alignment so I can see the coding (the Cs, As, Ts, and Gs).  I zoom in on a spot and when I put my mouse over the Rat code, it gives the number 10034062, when I cursor over the Mouse genome in the same spot, it gives the number 5312532.  I'm assuming these are the numbers for the position of that site within the chromosome. Correct, but it's not the same chromosome number. Why do you think that I tried to explain synteny to you?           Quote So, (if that's the case) it's not showing me the Rat and Mouse genomes, side by side - starting at position 10000001 and ending at position 10100000.  If it was, they'd both give the number 10034062 - wouldn't they? No, because contra your hypothesis, they aren't colinear. The autosomes are numbered according to their length, not their content. In fact, the place in which you were looking on rat chr10 has been inverted, and lines up with a bit of mouse chromosome 16, as VISTA tells you. These relationships are illustrated here: http://www.softberry.com/synt_pl....chr_2=* and in a different way, as well as conversely, here: http://www.informatics.jax.org/reports/homologymap/mouse_rat.shtml           Quote So, like I said, I'm not sure what I'm looking at and I'm not sure the correct way to use the site, but it doesn't appear to be giving me what I was looking for. Since your hypothesis is incorrect, what you're looking for doesn't exist. Rat chromosome 10 doesn't align with mouse chromosome 1, it aligns with chunks of mouse chromosomes 16, 17, and 11. Those represent translocations and inversions from the past. Therefore, none of those breakpoints have been conserved, and your hypothesis is incorrect. But all you had to do was look at the graph to see that between rat and mouse, there are big regions of no conservation between the pink lumps that are 80-100% conserved.           Quote So, if you have something you want me to see, you'll have to specifically tell me what it is I'm looking at and how it reflects on my hypothesis. Why are there gaps between the pink lumps that are the conserved sequences when we align orthologous sequences from two species within the same lineage? Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program. Let me ask you this: The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?   Does the VISTA program check for this?   Or does it only compare genes? -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 17 2007,18:37    Quote (swbarnes2 @ Oct. 16 2007,19:29)   Quote I made a specific prediction.  Why do you want me to modify it to fit your scenario? If your hypothesis is to be of any value, it has to be applicable to more than just one organism and one survival challange, surely you see that. So, 50 labs, 5 post-docs and techs a piece, selecting for resistance to a particular antibiotic, for 3 months. Do you predict that all the resistant strains found will carry the exact same resistance-granting mutation? No I don't.  Mainly because I think bacteria are designed to mutate and evolve quickly - so I'd predict a number of different mutations in that scenario. Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift. I'm interested to see JAMs data about the nylon though. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 17 2007,20:35    Quote (Daniel Smith @ Oct. 17 2007,18:31) Yes, I would be interested in seeing that.                 http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943 I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis. It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one.   Quote Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program. You're most welcome. How's your hypothesis? Quote The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner? It clearly was--it just wasn't conserved, as is clearly shown by the spaces between the pink humps of conserved sequences. Why are you not acknowledging my point about all the breakpoint sequences?   Quote Does the VISTA program check for this?   Specifically? No, but it answers your question clearly. The spaces between conserved sequences are mostly still there, but they aren't conserved. Do you understand that the spaces in between the conserved pink humps mean that your hypothesis is DOA? Quote Or does it only compare genes? It compares genomes. Genes are only a part of it.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 17 2007,21:03    Quote (Daniel Smith @ Oct. 17 2007,18:31) I'd like to see those - just for my own curiosity.     http://en.wikipedia.org/wiki/Telomere http://learn.genetics.utah.edu/features/telomeres/ http://users.rcn.com/jkimbal....es.html   Quote What is "contig"?       An assembly of overlapping sequences. Sometimes it's impossible to get overlap. Quote The rat genome appears to be a re-arrangement of the mouse genome,... The human genome just has many more (relative) rearrangements, as one would predict from evolutionary theory: http://www.informatics.jax.org/reports/homologymap/mouse_human.shtml Are you seeing anything in what I've shown you that is consistent with your hypothesis?

Steverino Posts: 411 Joined: Oct. 2005 (Permalink) Posted: Oct. 18 2007,06:34    "No I don't.  Mainly because I think bacteria are designed to mutate and evolve quickly - so I'd predict a number of different mutations in that scenario." You have no proof, evidence or data that the appearance of design, proves design other than you desire to have it be so. Whenever there is no current explanation for how something happened you play the design card.  I am glad the majority of science is not as lazy or stupid as you. -------------- - Born right the first time. - Asking questions is NOT the same as providing answers. - It's all fun and games until the flying monkeys show up!

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Oct. 18 2007,06:40    Quote (Daniel Smith @ Oct. 17 2007,18:37) Mainly because I think bacteria are designed to mutate and evolve quickly - so I'd predict a number of different mutations in that scenario. To what purpose? EDIT: E.G I designed a car so I could get around quickly. I designed a phone so I can stay in touch. I designed my home so I can live nice. I designed some bacteria to mutate and evolve quickly so I can.... -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

Richard Simons Posts: 425 Joined: Oct. 2006 (Permalink) Posted: Oct. 18 2007,08:35    Quote (oldmanintheskydidntdoit @ Oct. 18 2007,06:40) E.G I designed a car so I could get around quickly. I designed a phone so I can stay in touch. I designed my home so I can live nice. That's only partly true. After they were designed, someone had to build them. Who did (does?) the Great Designer co-opt to do the building, and how did they do it? Thinking about it more, I suppose the Designer sounds better than the Fabricator. (edited to correct grammar) -------------- All sweeping statements are wrong.

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Oct. 18 2007,08:54    Quote (Richard Simons @ Oct. 18 2007,08:35) Quote (oldmanintheskydidntdoit @ Oct. 18 2007,06:40) E.G I designed a car so I could get around quickly. I designed a phone so I can stay in touch. I designed my home so I can live nice. That's only partly true. After they were designed, someone had to build them. Who did (does?) the Great Designer co-opt to do the building, and how did they do it? Thinking about it more, I suppose the Designer sounds better than the Fabricator. (edited to correct grammar) Ah, interesting. Did the designer implement his own designs or did it sub-contract them out? ID is getting more like Hitchhikers every day :) -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

swbarnes2 Posts: 78 Joined: Mar. 2006 (Permalink) Posted: Oct. 18 2007,13:36    Quote No I don't.  Mainly because I think bacteria are designed to mutate and evolve quickly - so I'd predict a number of different mutations in that scenario. Don't you understand that when you are trying to prove that bacteria are designed, you can't take that as a given in that proof?   Quote Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift. Oh no.  This is just transparently dishonest.  You previously claimed that you predicted:   Quote Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72. Believe me, we all understand.  Creationists are constantly moving the goalposts.  It's inevitable for them if they want to pretend to be reasonable.  It's totally dishonest, but that's inevitable too. But to change the goalposts within, what, two days and one page of posts?  That's dishonest and sloppy.   Quote I'm interested to see JAMs data about the nylon though. It's not his data.  It's publicly available.  Surely the abstract, if not the whole paper, is available online. Why can't you look at the data yourself? Why didn't you look for the data before you made your claim?   Quote The rat genome appears to be a re-arrangement of the mouse genome, No, it doesn't appear to be that way. There was a common ancestor to both mice and rats.  Then those two lineages started evolving separate from each other.  Both lineages started getting both point mutations, and larger chromosomal rearrangments, inversions, duplications, etc. There are still swaths in both genomes where you can see the orignal sequences much as they were in the common ancestor.  But there are also parts where the mosue genome is unique, and the rat genome is unique. But to say the the two genomes are the same, but just rearranged is wrong. You would know that if you looked at the data before deciding what your conclusions were.   Quote so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?   Well, why can't you do the BLASTs that would prove this? Why does everyone else have to do the work to show that your imaginings aren't real? Honestly, who do you think is responsible for the accuracy of your biology claims? a) your mommy b) evil liberals c) strangers on a message board d) you We all think the answer is d.  We all think that if you make a claim about what the geomics of a mouse look like, that it is your responsibility to show that this is the case. That some people are being nice enough to educate your ignorant self doesn't change that fact. If you disagree, if you really think that you are not responsible for the truthfulness of your claims, can you explain a bit why you believe this?

blipey Posts: 2061 Joined: June 2006 (Permalink) Posted: Oct. 18 2007,14:01    Quote It's not his data.  It's publicly available.  Surely the abstract, if not the whole paper, is available online. Why can't you look at the data yourself? A. Not particularly interested in doing so? B. No recent experience looking for "data" so I don't know where to start? C. Data?  What's that? -------------- But I get the trick question- there isn't any such thing as one molecule of water. -JoeG And scientists rarely test theories. -Gary Gaulin

Henry J Posts: 5786 Joined: Mar. 2005 (Permalink) Posted: Oct. 18 2007,22:05    Quote C. Data?  What's that? The android on Star Trek: TNG. Henry

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 19 2007,18:14    Quote (JAM @ Oct. 17 2007,20:35)         Quote (Daniel Smith @ Oct. 17 2007,18:31) Yes, I would be interested in seeing that.                 http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943 I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis. It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one. While these results are interesting, they don't really meet the criteria of my prediction since they started with the already frame-shifted bacteria.  If you remember, my prediction involved the pre-frame-shifted bacteria Acromobacter guttatus.  My prediction was that if that bacteria was subjected to nylon, the same frame shift would occur. This study appears to involve a mutation of the Flavobacterium sp. strain KI72 - which already has the plasmid pOAD2 that was the result of the original frame shift. DISCLAIMER - I'm not calling you a liar or anything - I'm just hoping you can appreciate the difference from my perspective. - END DISCLAIMER         Quote             Quote Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program. You're most welcome. How's your hypothesis? It's not in as bad of shape as you think it is.         Quote           Quote The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner? It clearly was--it just wasn't conserved, as is clearly shown by the spaces between the pink humps of conserved sequences. Why are you not acknowledging my point about all the breakpoint sequences? In order to acknowledge that you are correct, I must first determine what exactly you're talking about, (no small task for me!), then I have to know what the parameters of VISTA are (does it ignore the non-coding sites? etc.), and finally I have to interpret these results in the light of designed descent.  If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.  I am not going to just throw up my hands and give up because you say so though!       Quote           Quote Does the VISTA program check for this?   Specifically? No, but it answers your question clearly. The spaces between conserved sequences are mostly still there, but they aren't conserved. Do you understand that the spaces in between the conserved pink humps mean that your hypothesis is DOA? No, I don't understand that - because there's no data showing me what those spaces represent.  The only thing I have to go on is your insistence that they falsify my hypothesis.   What I really need is a program that will... a.) allow me to select any region (coding or non-coding) of the mouse genome and b.) search the rat genome for a closely matching sequence. That's what I'd like to do.  Is there such a program?         Quote           Quote Or does it only compare genes? It compares genomes. Genes are only a part of it. Obviously I have much more research to do, but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity.  It's like taking a book, cutting up all the pages, shuffling them around and coming up with an equally coherent story. I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption? -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 19 2007,18:30    Quote (JAM @ Oct. 17 2007,21:03)   Quote (Daniel Smith @ Oct. 17 2007,18:31) I'd like to see those - just for my own curiosity.     http://en.wikipedia.org/wiki/Telomere http://learn.genetics.utah.edu/features/telomeres/ http://users.rcn.com/jkimbal....es.html Thank you.  Once again I'm amazed at the forethought of God!  Telomeres accomplish two things: they help to conserve genetic information while still guaranteeing that the aging process will eventually take its toll on all of us.  These might seem like contradictory functions to you, but they make perfect sense from my perspective.     Quote     Quote What is "contig"?       An assembly of overlapping sequences. Sometimes it's impossible to get overlap. No doubt.  The fact that there are such things as overlapping sequences makes me wonder at the mind of God.   Quote     Quote The rat genome appears to be a re-arrangement of the mouse genome,... The human genome just has many more (relative) rearrangements, as one would predict from evolutionary theory: http://www.informatics.jax.org/reports/homologymap/mouse_human.shtml Are you seeing anything in what I've shown you that is consistent with your hypothesis? Yes I am.  I know that's hard for you to believe, but the more mixed up these genomes are relative to each other, the more confident I am of a designed mechanism for that rearrangement. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 19 2007,18:34    Quote (swbarnes2 @ Oct. 18 2007,13:36)       Quote Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift. Oh no.  This is just transparently dishonest.  You previously claimed that you predicted:       Quote Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72. Believe me, we all understand.  Creationists are constantly moving the goalposts.  It's inevitable for them if they want to pretend to be reasonable.  It's totally dishonest, but that's inevitable too. But to change the goalposts within, what, two days and one page of posts?  That's dishonest and sloppy.   What's the difference between those two predictions? -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 19 2007,18:54    Quote (swbarnes2 @ Oct. 18 2007,13:36)     Quote so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?   Well, why can't you do the BLASTs that would prove this? "BLAST stands for Basic Local Alignment Search Tool. It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterised genes." (emphasis added) (link) I'm not interested in comparing genes. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Henry J Posts: 5786 Joined: Mar. 2005 (Permalink) Posted: Oct. 19 2007,22:06    Quote but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity. Why? Ours is already cut up into forty something pieces. Henry

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 20 2007,01:00    Quote (Daniel Smith @ Oct. 19 2007,18:14)   Quote (JAM @ Oct. 17 2007,20:35)           Quote (Daniel Smith @ Oct. 17 2007,18:31) Yes, I would be interested in seeing that.                 http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943 I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis. It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one. While these results are interesting, they don't really meet the criteria of my prediction since they started with the already frame-shifted bacteria.  If you remember, my prediction involved the pre-frame-shifted bacteria Acromobacter guttatus. First, if you'll do me the courtesy of rereading what I wrote, I noted that it is still bad news for your HYPOTHESIS, which is an accurate assessment. Your hypothesis makes many testable predictions, and your hypothesis is global, not just about one species. Second, frameshifts happen to individual genes. The term "frame-shifted bacteria" is gibberish.   Quote My prediction was that if that bacteria was subjected to nylon, the same frame shift would occur. But your hypothesis makes a very clear prediction in this case, too. Moreover, your prediction was based on a false assumption, because more than one enzyme is involved. In this case, we started without one of the two, and got a completely different new one from a different origin to replace its function. This falsifies your hypothesis. In case you've forgotten, here's your hypothesis, improperly stated as a prediction: Quote It's my prediction that random mutations are only neutral or deleterious - never advantageous.

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 20 2007,11:43    Quote (JAM @ Oct. 20 2007,01:00)   Quote (Daniel Smith @ Oct. 19 2007,18:14)     Quote (JAM @ Oct. 17 2007,20:35)               Quote (Daniel Smith @ Oct. 17 2007,18:31) Yes, I would be interested in seeing that.                 http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943 I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis. It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one. While these results are interesting, they don't really meet the criteria of my prediction since they started with the already frame-shifted bacteria.  If you remember, my prediction involved the pre-frame-shifted bacteria Acromobacter guttatus. First, if you'll do me the courtesy of rereading what I wrote, I noted that it is still bad news for your HYPOTHESIS, which is an accurate assessment. Your hypothesis makes many testable predictions, and your hypothesis is global, not just about one species. What exactly are these predictions? Quote Second, frameshifts happen to individual genes. The term "frame-shifted bacteria" is gibberish.     Quote My prediction was that if that bacteria was subjected to nylon, the same frame shift would occur. But your hypothesis makes a very clear prediction in this case, too. Which is? Quote Moreover, your prediction was based on a false assumption, because more than one enzyme is involved. Where specifically did I make this "false assumption"? Quote In this case, we started without one of the two, and got a completely different new one from a different origin to replace its function. This falsifies your hypothesis. How does this falsify my hypothesis? Quote In case you've forgotten, here's your hypothesis, improperly stated as a prediction:   Quote It's my prediction that random mutations are only neutral or deleterious - never advantageous. How do you know the mutation was random? -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 20 2007,13:24    Quote (Daniel Smith @ Oct. 20 2007,11:43) Where specifically did I make this "false assumption"?     When you assumed that only one gene and one mutation was involved. Quote Quote  In this case, we started without one of the two, and got a completely different new one from a different origin to replace its function. This falsifies your hypothesis. How does this falsify my hypothesis?   Because your hypothesis predicts that the same mutation will occur in the same gene. It's not limited to frameshifts or a single species. Your hypothesis is about living things in general. Quote How do you know the mutation was random? Because it was different than the initial one, and in an entirely different gene. Your hypothesis predicts that the same mutations will occur every time. You can't honestly weasel out of it by claiming that it only applies to one species and one gene.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 20 2007,13:25    Quote (Daniel Smith @ Oct. 19 2007,18:34) What's the difference between those two predictions? One says that the same thing will happen EVERY time, while the other says that the same thing will happen SOME of the time.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 20 2007,13:27    Quote (Daniel Smith @ Oct. 19 2007,18:54) I'm not interested in comparing genes. BLAST works for the sequences between genes, too, so your evasion doesn't work. That explanation is probably a holdover from the olden days, in which people were more interested in studying individual genes than they were in genomes. Most people still are more interested in the former, btw, you just wouldn't know it from the lay press.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 20 2007,14:14    Quote (Daniel Smith @ Oct. 19 2007,18:14)                       Quote                         Quote Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program. You're most welcome. How's your hypothesis? It's not in as bad of shape as you think it is. Interesting. How could you possibly know, since you claim below that you still don't understand what the VISTA graphs mean?                   Quote       Quote       Quote The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner? It clearly was--it just wasn't conserved, as is clearly shown by the spaces between the pink humps of conserved sequences. Why are you not acknowledging my point about all the breakpoint sequences? In order to acknowledge that you are correct, I must first determine what exactly you're talking about, (no small task for me!), Then how could you honestly claim that your hypothesis is not in bad shape, Daniel? I don't see how you can flip from certainty to ignorance and retain a shred of credibility.         Quote then I have to know what the parameters of VISTA are (does it ignore the non-coding sites? etc.), No, it does not ignore non-coding sites. In fact, you were looking at almost entirely non-coding sequences. How's your hypothesis doing?         Quote ...and finally I have to interpret these results in the light of designed descent. No, Daniel, that's utterly dishonest. You make your prediction BEFORE you interpret the data. Remember, you're trying to prevent yourself from fooling yourself.         Quote If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it. I don't believe you. Every prediction, explicit and implicit, from your hypotheses has been shown to be wrong, but you claim that it all supports your position.     Quote     Quote Specifically? No, but it answers your question clearly. The spaces between conserved sequences are mostly still there, but they aren't conserved. Do you understand that the spaces in between the conserved pink humps mean that your hypothesis is DOA? No, I don't understand that - because there's no data showing me what those spaces represent. Yes, there are data--the sequences themselves come up in the browser. What were you thinking they represented?         Quote The only thing I have to go on is your insistence that they falsify my hypothesis. My only insistence is that you examine the evidence, which you are desperately trying to avoid. Is there some reason why you can't read and/or comprehend the legend in the lower left corner?  Quote What I really need is a program that will... a.) allow me to select any region (coding or non-coding) of the mouse genome and b.) search the rat genome for a closely matching sequence. That's what I'd like to do.  Is there such a program? Yes, VISTA. You're so afraid of what you'll find that you won't explore it. If you need spoonfeeding, here's a larger region: http://pipeline.lbl.gov/servlet....llbar=0 1) Switch "# rows:" to 1. 2) Read the legend at lower left. See the symbol for genes? This region has four genes: Mtap7, Bclaf1, 260016C23Rik (a putative gene), and Pde7b. 3) Note the color of Exons in the legend: dark blue. See how the exons (protein-coding regions) are within the genes? The exons also are represented on the gene arrows at the top. Exons include all protein-coding regions, but they contain other sequences, such as UTRs, which have function. 4) Look at the scale for the Y axis on the right. It represents % identity. 5) Bonus question: why doesn't the scale go below 50%? 6) Do you see that the exons are highly conserved? 7) Do you see that there is less conservation outside the exons? 7) Look at the mouse vs. rat graph. These species are within the same "lineage" as you defined the term. What do the spaces between the pink bumps represent in that graph? If you'd like to browse, it's easiest to change chromosome number in the address bar. Here's a gene-rich region: http://pipeline.lbl.gov/servlet....llbar=0   Quote Obviously I have much more research to do, but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity. It's like taking a book, cutting up all the pages, shuffling them around and coming up with an equally coherent story. That's the power of selection. There's no coherent design hypothesis that can explain it.       Quote I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption? These *are* the data. There also are data from shorter time periods that, when extrapolated, are consistent with this.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Oct. 20 2007,14:29    Quote (Daniel Smith @ Oct. 19 2007,18:30) Thank you.  Once again I'm amazed at the forethought of God! Umm...then why did you assume that no telomeres were present, that you could just go in at base pair 1 with VISTA?   Quote Telomeres accomplish two things: they help to conserve genetic information while still guaranteeing that the aging process will eventually take its toll on all of us.  These might seem like contradictory functions to you, but they make perfect sense from my perspective. Yet your perspective predicted that they didn't exist. Can you name a part of the aging process in which telomeres don't work normally?   Quote   Quote   Quote What is "contig"?       An assembly of overlapping sequences. Sometimes it's impossible to get overlap. No doubt.  The fact that there are such things as overlapping sequences makes me wonder at the mind of God. How do you figure? Contigs and overlapping sequences merely describe the assembly of sequences by humans. You'll say anything to avoid testing your own hypotheses against the evidence, won't you?     Quote   Quote Are you seeing anything in what I've shown you that is consistent with your hypothesis? Yes I am.  I know that's hard for you to believe, but the more mixed up these genomes are relative to each other, the more confident I am of a designed mechanism for that rearrangement. How can you be confident when you've predicted the polar opposite in all these cases?

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 20 2007,18:35    From Wikipedia: Quote Recent evidence suggests that "junk DNA" may in fact be employed by proteins created from coding DNA. An experiment concerning the relationship between introns and coded proteins provided evidence for a theory that "junk DNA" is just as important as coding DNA. This experiment consisted of damaging a portion of noncoding DNA in a plant which resulted in a significant change in the leaf structure because structural proteins depended on information contained in introns. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 20 2007,19:09    Quote (JAM @ Oct. 20 2007,14:14) Yes, VISTA. You're so afraid of what you'll find that you won't explore it. If you need spoonfeeding, here's a larger region: http://pipeline.lbl.gov/servlet....llbar=0 1) Switch "# rows:" to 1. 2) Read the legend at lower left. See the symbol for genes? This region has four genes: Mtap7, Bclaf1, 260016C23Rik (a putative gene), and Pde7b. 3) Note the color of Exons in the legend: dark blue. See how the exons (protein-coding regions) are within the genes? The exons also are represented on the gene arrows at the top. Exons include all protein-coding regions, but they contain other sequences, such as UTRs, which have function. 4) Look at the scale for the Y axis on the right. It represents % identity. 5) Bonus question: why doesn't the scale go below 50%? 6) Do you see that the exons are highly conserved? 7) Do you see that there is less conservation outside the exons? 7) Look at the mouse vs. rat graph. These species are within the same "lineage" as you defined the term. What do the spaces between the pink bumps represent in that graph? If you'd like to browse, it's easiest to change chromosome number in the address bar. Here's a gene-rich region: http://pipeline.lbl.gov/servlet....llbar=0 First, thanks for making it a bit clearer. Second, if the protein coding regions are dark blue and UTRs are light blue, what are the pink (CNS) regions? Are these non-coding?   If so, why are they also so highly conserved between rat and mouse? Like this?         Quote Quote Obviously I have much more research to do, but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity. It's like taking a book, cutting up all the pages, shuffling them around and coming up with an equally coherent story. That's the power of selection. There's no coherent design hypothesis that can explain it. Sure there is.  Every kid who ever rearranged someone else's book report to try to "put it in his own words" knows about it. BTW, giving credit to "selection" without showing the steps that were selected for is only an assumption and is not grounded in the evidence.   Quote                 Quote I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption? These *are* the data. There also are data from shorter time periods that, when extrapolated, are consistent with this. Isn't that the classic case of using the thing that must be explained as an explanation?  I was told that was taboo around here. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 20 2007,19:15    Another example. In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 20 2007,19:18    Oops!  When I click on the links I just provided, they take you to the page JAM originally pointed me to - not the pages I created in VISTA. I'll have to figure out how to get the correct URL. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

Daniel Smith Posts: 970 Joined: Sep. 2007 (Permalink) Posted: Oct. 20 2007,19:22    Try this. -------------- "If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright "The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

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