JAM
Posts: 517
Joined: July 2007
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| Quote (Daniel Smith @ Oct. 19 2007,18:14) |
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| 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.
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