Totally useless info. Doesnt address any of my points and always manages to get in some mocking. This is why I debate with Alate and not you.
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Totally useless info. Doesnt address any of my points and always manages to get in some mocking. This is why I debate with Alate and not you.
Flipper
New member
As you're still posting on the thread, I thought I'd bring this back up for your attention; as you may have missed it the first time.
No wonder, the way you read. Anyway, I am happy for you to have another chance to elaborate on the following:
Well, not really - its an explanation that's "not good" because it doesn't match any observed reality for a large number of reasons. In this particular case, just one will do because because it's as apropos as it is fatal to this particular argument. It also happens to be great evidence that you don't do any research before you run your proudly ignorant mouth with whatever conjecture takes your fancy, as if that constituted evidence.
No, it's an important point. Alligators should be closer genetically (and thereby biochemically) to penguins than they are to snakes. Alligators and birds are archosaurs, and have a last common ancestor, after that ancestor had diverged from other reptiles. Hence you should see the phylogenies that way.
Molecular evidence for the origin of birds
(evolution/tpod/amniote/phylogeny/systematics)
S. BLAIR HEDGES
Department of Biology and Institute of Molecular Evolutionary Genetics, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802
Communicated by Charles G. Sibley, December 9, 1993
ABSTRACT The major groups of amniote vertebrates
appeared during a relatively short time span at the end of the
Paleozoic Era, a fact that has caused difficulty in estimating
their relationships. The fossil record suggests that crocodilans
are the closest living relatives ofbirds. However, morphological
characters and molecular sequence data from living amniotes
have repeatedly chaflenged this hypothesis by indicating a
bird-mammal relationship. DNA sequences from four slowevolving
genes (mitochondrial 12S and 16S rRNA, tRNAVaI,
and nuclear a-enolase) now provide strong statistical support
for a bird-crocodillan relationship.
http://www.pnas.org/content/91/7/2621.full.pdf
Just clearing something up.
Don't see that. I'm thinking you infer a lot that isn't there, sometimes.
Feel free. I'm just dropping in a comment when I see something worth a remark.
Feel free to actually share one of these "reasons". :chuckle:
And feel free to make that concession that "Kind" is clearly defined and "Species" is vague and malleable.
You cherry pick which genomes you compare, and how they are compared.
Thanks for agreeing with me. Now carry that to a logical conclusion and admit evolution needs to investigate the stepping stone problem. Because what we know now, scientifically, is that the stepping stone problem is likely.
Alate_One
Well-known member
You don't cherry pick "how they are compared". I showed you the figure, the only comparison that was made was how many nucleotide differences there are from one sequence to another. That's why the scale is simply in "substitutions per 100 bases. That's a simple comparison anyone can do admittedly genomes are too large to do without a super computer.
Why haven't you done the DNA comparison I posted for yourself, it uses the exact same method and you can do it yourself to be sure there's no bias.
You don't think the species on the list were a reasonable sample of placental mammal diversity?
You can keep asserting this forever, but you don't have the information to say it is a problem. We have known that evolution happens and the earth is old from long before we had any idea of DNA data. Deal with it.
How about you admit that you'll never accept evolution, no matter what data is presented. You'll claim it's biased or move the goal posts every time.
How is the base nucleotide sequence determined? Is it the sequence from an individual or is it a composite sequence? How is that composite composed? Are both organisms sequenced in the same fashion?
There are plenty of ways you could find similarities and differences to varying extents between two sets of data by choosing how that data is presented.
Alate_One
Well-known member
For humans I believe it was a composite (though we are now accumulating many sequences from individuals), for most other organisms likely a single individual.
It's a simple comparison Stripe.
like this:
ATAGGACCATAGA
ATAGCAACATAGA
How many differences are there between the two sequences above?
Now imagine doing that over 3 trillion bases. That's how it is done. Since it's done with computers that use the same settings throughout the comparison, it's rather hard to claim bias. Especially when this comparison and dozens of others based on other data come up with the same answer.
In fact you can even play a flash game to line up bases. It's a bit more complicated when gaps have to be inserted, but there are settings for the size and length of the gap that stay consistent.
So for the studies you point to?
Two.
How many differences with this one?
ATAGGACCATAGA
TAGCAACATAGAA
:chuckle:
Somewhat blunt force and unsophisticated, not to mention a totally useless means of determining similarity.
I don't for a second believe that is the only method for comparing how similar two sequences are.
A computer is only able to do what it has been programmed to do. If it has been tasked with looking for similar sets of nucleotides then that's what it will come back with. If it is assigning percentages according to certain criteria then that is what it will do. If those criteria are changed, its output will change.
Pretending a computer removes our ability to manipulate numbers is rather naive of you.
Of course it is.
I see Stipe is out of excuses again. Suddenly, he decides genetic sequences aren't a good idea after all.
Guess why.
Guess why.
Alate_One
Well-known member
What I said already.
Oh my, he can count! :chuckle:
One insertion at the end, deletion at the front, two substitutions. So four if you scored the changes equally, which you wouldn't. An alignment optimizes the number of matches overall while strongly penalizing gap insertion. A scoring system is used to determine which fit is best, the same scoring system is used in the game I linked.
Why because you say so? How would you determine similarity?
No, I'm saying that it keeps whatever assumptions there are consistent. You can't skew it to one sequence or another.
And yet only one change is required in order to make one into the other.
With information, you need more sophistication than the brute force method you apply to determine similarity.
Because two information sets can be wildly different in form, yet produce the same result.
You're not telling the whole truth. There has to be more to the comparisons than the brute force, straight up comparison you've presented. There must be some preparation of the data going on. A straight up comparison will give you results, but nothing of any value.
This is amply demonstrated in my counter to your "two differences" example. I moved a single letter and created a far worse result for your similarity measure when to any informed reader, the change was less affective.
Try this one:
ainbowr
painnow
As you can see, an English reader is more easily able to discover the word intended in the first case even though, according to your measure, the second case is more similar to the answer (rainbow).
Alate_One
Well-known member
No, you did more than one change. You moved one letter from one end to the other but DNA fragments of Eukaryotes aren't circular (same mtDNA) so that's two changes (a deletion and insertion). Plus the one you changed already had two changes compared to the other, so four changes. Your attempt at deception failed. :chuckle:
What "preparation" would you assume? DNA data is just long lines of As, Ts, Gs and Cs. There needs to be an alignment of the sequence before differences can be determined. Repetitive regions of DNA may be excluded (regions of aag aag repeated over and over for example) The tree is drawn based on the results, the differences between the sequences once aligned, taking into accounts insertions and deletions.
But for handfuls of genes or regions the only preparation I did was pasting into forms. You might change settings if you know what you're doing. I just reported the settings I used.
Your example has nothing to do with DNA sequences since if you change the order you destroy the meaning extremely quickly in DNA. In English different order doesn't have to destroy meaning. Apples to oranges.
For example if the two were translated:
ATAGGACCATAGA equates to: I G P Stop
and TAGCAACATAGAA equates to: Stop Q H R
With JUST a flip of letters compared to the other as you should have done:
TAGGACCATAGAA equates to: Stop N H R
One flip of letters and the meaning is totally different. Really with a stop in front the meaning would be obliterated. Totally contrary to the rules of English. Please come back when you have some idea what you're talking about. KTHXBAI :dog:
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Well, let's test Stipe's idea.
Stipe, here's two sequences:
1010101010101010101
1100110101100011011
Tell me the information content of the first one and the second one. Show your work. If you don't know enough about information to calculate the two, just tell us which one has more information and how you know.
And if you can't do a simple information problem like that, what makes you think you know enough to discuss information?
Stipe, here's two sequences:
1010101010101010101
1100110101100011011
Tell me the information content of the first one and the second one. Show your work. If you don't know enough about information to calculate the two, just tell us which one has more information and how you know.
And if you can't do a simple information problem like that, what makes you think you know enough to discuss information?
No deception. Two changes.
And the point stands.
Alignment of the sequence before differences can be determined. Repetitive regions of DNA may be excluded. Stuff like that.
Great. Now imagine if the translator knew to start reading one letter in and the next letter on after the sequence was an "A".
Not if you know what you're looking for.
OK, thanks. Bye. :wave:
Alate_One
Well-known member
You used my altered sequence to make the change. And then asked me to compare it to the first. Oops.
Except the translator AKA the Ribosome doesn't know that. The type of change you made is called a frameshift
The cell doesn't know, and you don't have a clue.
Flipper
New member
And with only the addition of a space, you get two entirely new words, both with completely different functions.
pain now
I guess happy accidents can occur that can result in new information.
Oops. Right you are. It should have been this:
ATAGGACCATAGA
TAGGACCATAGAA
The point stands. The same number of changes, vastly greater difference in similarity according to your brute force method.
What does that matter? The sequence might still be present and a candidate for comparison.
Of course it is.
The cell doesn't need to know. In a sequence of 109 randomly generated ATGCs, the (corrected) frameshift sequence I gave will show up about 50 times. If you are to pick out those and compare them to the original you will meet the problem I am describing.
Information cannot be reasonably compared using the brute force method you are describing.
Actually, I do. You might want to start elaborating instead of dropping off the kindergarten lesson and pretending that settles things.
Which would only ever destroy the intended meaning.
"Somewhere over the rainbow" v "Somewhere over the pain now".
Yeah. Information. :chuckle:
And with only the addition of a space, you get two entirely new words, both with completely different functions.
Stipe mutters:
And produce a different one. Which is exactly what evolution does. In the case of Hall's bacteria, for example, the "intended meaning" of a duplicated gene was "destroyed", and in it's place a useful new enzyme was evolved.
How about that? Mutations always produce new information, and sometimes, it's useful new information.
Natural selection handles the rest.
Stipe mutters:
And produce a different one. Which is exactly what evolution does. In the case of Hall's bacteria, for example, the "intended meaning" of a duplicated gene was "destroyed", and in it's place a useful new enzyme was evolved.
How about that? Mutations always produce new information, and sometimes, it's useful new information.
Natural selection handles the rest.