A new paper by dr tomkins try to disprove that claim about the vitellogenin pseudo gene


(Dcscccc) #1

a new paper by dr tomkins try to disprove the claim about vitellogenin:

in short: dr tomkins find that:

1)this partial sequence is actually in the center of a functional gene called "gam"
2)this short sequence is too short to conclud its a remain of a vtg gene (less then 1% similarity from the whole gene)
3)this sequence is too conserve to be a non functional


#2

This is just pathetic.

The first sentence of the results, your point number 2, is just plain false:

Is Tomkins simply unable to understand that only one of the many exons was shown in Supplemental Figure 2 (to show shared indels) of the 2008 paper, or is Tomkins trying to deceive his readers?


(Dcscccc) #3

joao, here is the original paper from 2008:

figure 2 show that he is talking about the whole genes and not just some exons. and what about the fact that this “vgt” is in the center of the gam gene? if its true how we can even call it a pseudo gene?


#4

Yes, it should have been obvious that I was referring to that paper. Why are you pretending that I didn’t look at it, when the issue is that you claimed that Tomkins disproved the claim without bothering to look at the claim or the evidence to support it?

Exons of which gene(s) specifically? VIT1, VIT2, and/or VIT3? Where does the number 150 come from? Be precise. Look at the evidence for yourself, if you dare…


(Dcscccc) #5

we talking about vit 1 because the similarity of vit 2 and 3 is too low according to the paper. so from the vit1 we only have near 150 base match. its too low.


#6

Good, let’s talk about VIT1. Where do you get the 150 figure from the 2008 paper? Remember, YOU said “according to the paper.”

Look at the top of Figure 2. How many exons does VIT1 have? How many introns? How many exons show homology? How many introns? How many bases total?

Why doesn’t Tomkins call VIT1 VIT1?


(Dcscccc) #7

i mean according to the paper of tomknis. i dont chack how many bases this contain. i do remember that its something like several percent. do you have any other source that show something else?

from what i can see figure 2 at the 208 paper show the entire genes and not just several exons. so again- what do you mean?


(sy_garte) #8

@Joao

Based on this and similar “papers” from this author, I tend to favor the latter explanation.


#9

[quote=“dcscccc, post:7, topic:3198, full:true”]
i mean according to the paper of tomknis.[/quote]
So you really have absolutely no business claiming that Tomkins disproved anything.

You restated Tomkins’s claim but you have no clue why he made it. Is it ethical for you to claim that he disproved anything when you are unable or unwilling to dip even a toe into the evidence?

You can’t find any evidence for Tomkins’s claim in the 2008 paper. Tomkins claims that as his source.

[quote]from what i can see figure 2 at the 208 paper show the entire genes and not just several exons. so again- what do you mean?
[/quote]How many exons are in the VIT1 gene? We already agreed to focus on one gene, remember?


(Dcscccc) #10

ok.lets focus in the vit1 gene. this gene contain 35 exons and more then 20000 bp:

how many of this share between chicken and human?


#11

The answer is in the top panel of Figure 2–every place there’s a black dot in the VIT1 gene. The first of those dots is 150 bases long and is shown in Supplemental Figure 2.

So I’ll ask again: is it ethical for you to claim that Tomkins disproved anything when you never bothered to look at the evidence? Don’t you think a retraction is in order? At least until you understand the data?

Where did the number 150 bases come from? You thought it was important enough to cite in your claim that Tomkins had proven his point.


(Dcscccc) #12

hi joao. first- you may right about the topic claim (i actually said in my first coment that tomkins try to disprove).so i changed the topic name now.

now about the vit1- i think we can both agree from figure 2 that there is less then 10% similarity compere to the chicken vit1. so again- how do you know its a real remains and not something else?

dr tomkins take the 150 number from is research. again- do you have a different number prove that dr tomkins was wrong?


#13

[quote=“dcscccc, post:12, topic:3198, full:true”]
hi joao. first- you may right about the topic claim (i actually said in my first coment that tomkins try to disprove).so i changed the topic name now.[/quote]
Good.

No, I think what’s obvious is that you don’t know how to read the figure and that you won’t admit that Tomkins made a false claim when he cited that paper in support of only 150 bases.

Why do the black dots form a diagonal line across the graph?

That’s false. He said that it’s from the 2008 paper, and neither of us can find it there. It’s a fabrication.

[quote] again- do you have a different number prove that dr tomkins was wrong?
[/quote]I just showed you that he is wrong and you demonstrated it to yourself. You made the claim, too, with absolutely nothing to support it.


(Dcscccc) #14

joao. i think dr tomkins take is number from here:

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr1%3A79254632-79254781&hgsid=451231637_gOL4acye0kipRYRajhRsr8GAmR8D

and he doesnt said that he take it from the article (if yes show me where).

i look again in figure 2 and i dont see any real similarity between the vit1 of human and chicken. no more then 10%. so again- what is the specific number (in terms of percent) about the similarity?


#15

False. Nothing about homology there.

[quote=“dcscccc, post:14, topic:3198”]
and he doesnt said that he take it from the article (if yes show me where).[/quote]
Unbelievable.
“The sequence identified by Brawand, Wahli, and Kaessmann (2008) as being a vtg pseudogene is only 150 bases long…”

How did you calculate that number?

[quote] so again- what is the specific number (in terms of percent) about the similarity?
[/quote]You made an explicit claim! It’s up to YOU to support or retract it!

Again, why do the black dots form a diagonal line across the graph? If you can’t explain that, you have no idea how to read the figure.


(Dcscccc) #16

“The sequence identified by Brawand, Wahli, and Kaessmann (2008) as being a vtg pseudogene is only 150 bases long.”-

where is said he take the 150 number from the article? he said that the sequence is about 150 base long. but he doesnt said that it take it from their article.

'How did you calculate that number? "-

you can see and compare the black dots with the whole sequence from the chicken above it. we can see that it isnt more then 10% similarity.


#17

No, you don’t understand. What’s the criterion for a black dot, and why do they go along a diagonal? You shouldn’t be making any claims about who proved what without being able to understand something so basic.


(Dcscccc) #18

last time- he take it from is own research.

now lets talk about the vit1:the graph represent the chicken seq vs the human one. what is your point?


#19

[quote=“dcscccc, post:18, topic:3198, full:true”]
last time- he take it from is own research.[/quote]
What research?

[quote]now lets talk about the vit1:the graph represent the chicken seq vs the human one. what is your point?
[/quote]My point is that you don’t understand it. You can learn by trying to answer questions:

  1. Why do the black dots line up diagonally?
  2. If we make two random DNA sequences, what percent identity do we expect them to have?

If you can answer #2, you’ll realize how your “10% similarity” shows that you don’t have the slightest idea about what you’re talking about, starting with the fact that “similarity” doesn’t apply to nucleotide sequences, only protein sequences.


(Dcscccc) #20

i will answer to your point 2- we can predict that bacause there is 4 kind of nocleotides, in a random sequence of 1000 bases we will get something like 250 matchs. or about 25% similarity.