Similarity of human and chimp DNA is down.

[Blayz]

My point is that there is a statistical match in the Uncommon Decent article giving it credibility in its method.

Right...so the uncommon descent gain credibility for agreeing with with general evolutionary studies. Funny stuff.

When taken segment on segment you only find they are an exact match 62.5% of the time, I maintain you can not call two genomes 98% equivalent if they do not compare segment for segment 98% of the time;

But you maintain this in the absence of credibility, sense, statistics, math and biology. You have even printed the formula which explains why a 62% segment match equates to 98% similarity. Moreover, you are alone on the planet in believing this to be correct. Even the author of the paper does not agree with you.

Have you considered joining the rest of humanity in this?

the 98% conclusion in the chimp paper is just a bogus evolution fairytale. The problem is that the evolutionist is being misleading in an accurate Interpretation.

It's the same conclusion as found in the uncommon descent paper. THE EXACT SAME CONCLUSION. The only one being misleading here is you.

By the way the Uncommon Decent analysis used the pre-aligned segments of the chimp genome study from the Web and of course statistically they better match. But how on earth do you get from 98% similar to the real statistical value of 62.5% similar?

You have got to be kidding me. You have been throwing poisson around like there is no tomorrow. You have already shown yourself how you get 98% similarity. Are you honestly telling me you actually have no understanding of statistics at all? How disappointing.

By the way arguments against a published work is considered criticism and because they get criticism that does not mean they are wrong.

But they are wrong. Their data is based on there being 60000 genes in the human genome instead of the ~20000 that there actually is.

They are, actually, completely wrong, and since their calculations are based on incorrect data, it means the calculations are wrong too.

I think scientists, at least some, care about truth also.

Ironically, we do. Which is why we fight so hard against your disinformation and misunderstandings

 

[Zaius137]

Your fun….

“But you maintain this in the absence of credibility, sense, statistics, math and biology. You have even printed the formula which explains why a 62% segment match equates to 98% similarity. Moreover, you are alone on the planet in believing this to be correct. Even the author of the paper does not agree with you.”

Well since you know every mind on the planet how can I reason against a universal mind.

Here is what the Uncommon Decent article actually says about the findings:

“However, if the two genomes were really 95% similar or more, as is commonly claimed, also a 30BPM statistical test should produce 95% results, and it does not.”
I guess it all depends on the definition of “not”… right?

“You have got to be kidding me. You have been throwing poisson around like there is no tomorrow. You have already shown yourself how you get 98% similarity. Are you honestly telling me you actually have no understanding of statistics at all? How disappointing.”

Sorry but as all good evolutionists you are misrepresenting the facts…98% =/= 62%, even I can get that right. Now you finally acknowledge I am using the poisson distribution; just a few threads ago you did not recognize it… What kind of scientist are you? or are you a scientist? Maybe you are just a layman as I am.


“But they are wrong. Their data is based on there being 60000 genes in the human genome instead of the ~20000 that there actually is.”

“They are, actually, completely wrong, and since their calculations are based on incorrect data, it means the calculations are wrong too.”

I need your citation on this please…

 

[Blayz]

Well since you know every mind on the planet how can I reason against a universal mind.

Start small. Try reasoning against just one mind, and go from there.

Here is what the Uncommon Decent article actually says about the findings:

“However, if the two genomes were really 95% similar or more, as is commonly claimed, also a 30BPM statistical test should produce 95% results, and it does not.”
I guess it all depends on the definition of “not”… right?

Not really, It does however display a certain level of either inability to comprehend, laziness, or malicious intent to misinform

A linear interpolation can work as first approximation in a short range. If in my ESM model we consider two genomes differing 2% we have M=40%. This way we have two points of the interpolation line: (99,70) and (98,40). The relative equation is 30X – Y = 2900 (where X are the normalized 30BPM similarities and Y are the un-normalized ones, those I show in the table and graph). If Y=62 (the median at the right-bottom of the table) we get from the equation X=98.73%.
Therefore we have two normalization methods (yours binomial non-linear, mine linear) that agree as final result.

(empahsis mine)

Sorry but as all good evolutionists you are misrepresenting the facts…98% =/= 62%, even I can get that right. Now you finally acknowledge I am using the poisson distribution; just a few threads ago you did not recognize it… What kind of scientist are you? or are you a scientist? Maybe you are just a layman as I am.

No, it's you that is misrepresenting the facts, from not understanding the application of poisson to misrepresenting the null case as the formula for poisson...actually, it might be that you don't understand normalization.

I need your citation on this please…

Citation on what, the number of genes in the human genome?

Here's one from 2007
CellNEWS: How Many Genes in the Human Genome?
and one from 2008
Human Genome Project Science

If you download the xref table from the UCSC browser it comes to 29000, but that includes pseudogenes, non coding and micro RNA.

 

[Zaius137]

Man are you upside down on this one…
"(empahsis mine)"

I believe you don’t understand what you are looking at. You are so eager to maintain your evolution argument that you are doing sloppy research.
From what I understand the author is trying to normalize his 30bp test to higher coincidences in an ESM couple of 99% equal genomes. To figure this out you have to go back to his justification in (#73 Uncommon Decent). From what I understand the author is using the argument that a linear relationship exists so he can simply apply a linear proportionality to accommodate the data. The X= 98.73% was a given value not calculated from the authors treatise.
Do you see the conclusion in last sentence of (#73 Uncommon Decent)… it reads 88%. The author makes note that this would be considered liberal evaluation.
Even when normalized the figure is only 88% probability for the extreme match cases…

All you have to do is read the bottom of point (#78 Uncommon Decent)
“As a consequence the normalized result of the 30BPM test in no way supports the evolutionist claims of a common ancestor of these genomes. A blind evolution that changes and scrambles 38 millions bases is unthinkable.”
That is my point exactly…

 

[Blayz]

Man are you upside down on this one…
"(empahsis mine)"

Umm, you didn't include any emphasis.

I believe you don’t understand what you are looking at. You are so eager to maintain your evolution argument that you are doing sloppy research.

From what I understand the author is trying to normalize his 30bp test to higher coincidences in an ESM couple of 99% equal genomes.

You understand incorrectly. What the author is trying to do is to normalize his method so that it is comparable to other methods, which is pretty much the definition of normalization. He is in fact attempting to normalize the results from his 30BP method so that they can be compared to those from a 1 BP method.

To figure this out you have to go back to his justification in (#73 Uncommon Decent). From what I understand the author is using the argument that a linear relationship exists so he can simply apply a linear proportionality to accommodate the data. The X= 98.73% was a given value not calculated from the authors treatise.

Again, you understand incorrectly. The X=98.73% was directly calculated from the author's treatise, utilizing a linear approximation to the poisson distribution, the differential at an appropriate point of the curve, to be precise.

Do you see the conclusion in last sentence of (#73 Uncommon Decent)… it reads 88%. The author makes note that this would be considered liberal evaluation.

Indeed, a rebuttal he retracs through comments #74 to #78, when he realises the 88% was wrong.

All you have to do is read the bottom of point (#78 Uncommon Decent)

“As a consequence the normalized result of the 30BPM test in no way supports the evolutionist claims of a common ancestor of these genomes. A blind evolution that changes and scrambles 38 millions bases is unthinkable.”
That is my point exactly…

This is nothing more than the author's inherent bias against evolution. It is a conclusion that has nothing to do with the evidence that has been collected, even by the author himself. It is, to all intents and purposes, a hissy fit.

Is this is really your point? That I should only read the conclusion and not look at the evidence to support it?

By the way, I see nothing "unthinkable" about a blind evolution that changes and scrambles 38 million bp, which represents about 0.1% of the two genomes.

 

[Nostromo]

I have a feeling that this thread would benefit from more pictures.

 

[Blayz]

I have a feeling that this thread would benefit from more pictures.

I was thinking more cowbell

 

[Zaius137]

Blayz…

You know I would like to keep this discussion intellectually honest but it seems you will not have it. You are actually trying to show a creationist article supports an evolutionist human/chimp comparison. That is funny.

“You understand incorrectly. What the author is trying to do is to normalize his method so that it is comparable to other methods, which is pretty much the definition of normalization. He is in fact attempting to normalize the results from his 30BP method so that they can be compared to those from a 1 BP method.”

Fill me in on the 1BP method, if you are talking a wild comparison bp per bp that would severely damage the higher match estimate because of all the erroneous insertions and deletions that had to be made to even the lengths of the chromosomes.

“Indeed, a rebuttal he retracs through comments #74 to #78, when he realises the 88% was wrong.”

You have got to be kidding me… How can you misrepresent the wording when everyone can read the posts for themselves?

This discussion has played out like many others with evolutionists; when they can no longer pose a reasonable argument they just make things up.

This from #74…

“You are right that homologies between living forms point to a unique Designer. There is more. As it was said: “In any thing [not only life] there is a sign that He is unique”. In the same time there are astonishing differences between living forms in particular (and between all things in the universe) but this evidences the immensity of His creative power.”

Your arguments are at best bizarre. I will let the author state his own conclusion.

The authors last words in the article (quote)..

A simple layman’s statistical test, such as the 30BPM, shows that the “95% claim” described above is a highly controversial one. It is worth noting that as more information comparing the two genomes is published, the differences between them will appear more profound than they were originally thought to be. The big question that still remains is: what should one conclude from the similarities and differences between the genomes of humans and chimpanzees? Commonly reported evolutionary statistics that should provide an informative answer to this question may actually obscure the true answer.

Read my very first posting…

 

[Nostromo]

You have got to be kidding me… How can you misrepresent the wording when everyone can read the posts for themselves?

I just read it myself, the last figure he gives is clearly 98.73% (#78), whereas before he was claiming 88% (#73).

As you say, it's right there for everyone to read, so why is it so damned hard for you?

 

[Blayz]

Blayz…

You know I would like to keep this discussion intellectually honest but it seems you will not have it. You are actually trying to show a creationist article supports an evolutionist human/chimp comparison. That is funny.

On the contrary, I am trying to show no such thing. I am simply trying to show you that the methodology employed by the author arrives at very similar results as achieved by others, and that throwing around an un-normalized value such as "62%" is wrong.

Fill me in on the 1BP method,

There are many of them. Jukes and Cantor and Kimura for distance methods, maximum likelihood and parsimony are others. What they all have in common is they present a per base mutation/divergence/similarity rate.

if you are talking a wild comparison bp per bp that would severely damage the higher match estimate because of all the erroneous insertions and deletions that had to be made to even the lengths of the chromosomes.

Whilst I would agree that none of these methods (the Uncommon descent paper included) deal with indels, it is irrelevant in the context of the question, which is how does the normalized result from the uncommon descent paper compare to the normalized results of other similar methods.

And note, although per bp is the accepted presentation, there is nothing to stop you from taking the per 30BP as the standard and normalizing the other methods to it. It doesn't matter which direction you go in, so long as you state it clearly.

You have got to be kidding me… How can you misrepresent the wording when everyone can read the posts for themselves?

What do you mean? He clearly gives up the 88% in favour of the 98.73%.

This discussion has played out like many others with evolutionists; when they can no longer pose a reasonable argument they just make things up.

I understand by this point you are getting desperate. Much like the author you thought that statistics would be on your side when quite clearly they are not. However, if it helps, I agree with the other correspondent in the comments section who basically said that similarity does not mean common descent.

This from #74…

“You are right that homologies between living forms point to a unique Designer. There is more. As it was said: “In any thing [not only life] there is a sign that He is unique”. In the same time there are astonishing differences between living forms in particular (and between all things in the universe) but this evidences the immensity of His creative power.”

This is wishful speculation, it has no bearing on nor connection to the work presented in the paper. It wouldn't mater what results were obtained, the above paragraph could have been added.

The authors last words in the article (quote)..

A simple layman’s statistical test, such as the 30BPM, shows that the “95% claim” described above is a highly controversial one.

Ahh yes, so you ignore all the comments, the parts where the author changed his analysis. You are just going to ignore them, and go back to the original article. Like a child sticking his fingers in his ears and yelling "nyah, nyah, I can't hear you".

That's truly intellectually dishonest.

 

[Zaius137]

The author concedes no such thing the X=98.73% was the normalization reference to the evolutionist's findings of 98.73% and was the given (X) to validate the two methods of normalization, one linear the other non-linear. The author’s Y value is his real findings; he is only demonstrating that if you assume a higher evolutionist finding his Y value has to be normalized to a higher value. In other words he demonstrates that for assuming a higher X value the 30bp method would have to find a higher Y value (but he found 62%).

The 30X-Y = 2900 is a linear track and verifies that if you increase X to 99% you must find a Y (30bp) of 70%. Try it yourself. Remember his linearity justification only works for small delta X’s. I am not convinced his extrapolation is linear. I prefer the poisson distribution. Non-linear...

Don’t buy into Blayz’s math you will only get confused.

 

[Blayz]

The author concedes no such thing the X=98.73% was the normalization reference to the evolutionist's findings of 98.73%

There is no "evolutionists findings" of 98.73% It comes purely from the application of a linear approximation to his 62% of 30BP. It is (or would be if he'd used poisson), the 30th root of 0.62. Stick it in a calculator, see what you get.

The irony is if he'd used poisson he'd have gotten the more accurate value of 98.41%. 98.73% is an over estimation.

Try it yourself. Remember his linearity justification only works for small delta X’s. I am not convinced his extrapolation is linear. I prefer the poisson distribution. Non-linear...

Well it had to happen I guess. You have said something I agree with entirely. From my reading, the only reason the author used the linear approximation is hubris at being told to normalize in the first place by the other guy posting in the comments.

Don’t buy into Blayz’s math you will only get confused.

Not my method. I am simply stating what the author himself did in the comments attached to his own article. His (lets face it crazy) linear approximation is a way to normalize a 30BP result to 1BP.

You have to see this is needed. I don't understand how you can have an understanding of statistics but a complete blind spot of how to apply them.

if you assume a higher evolutionist finding his Y value has to be normalized to a higher value.

That's not it at all. It's not being normalized to a higher value, it's being normalized to a different metric, from a 30BP metric to a 1BP metric.


If the author had used 20BP instead he would have gotten another number (~72.7). If he'd used 50BP it would have been lower (~45.1). The only way to reconcile these basically arbitrary blocks is to bring them all back to the same scale.

Other wise what you are saying is that 50 miles/hr is less than 51 km/hr simply because 50 is less than 51. If you don't normalize the data, you cannot compare it.

I spend half my life normalizing heterogeneous datasets, I do know what I am talking about.

 

[Zaius137]

Maybe if you spent half your life studying mathematics you would fair better.

A comparison of 98.73% bp similarity yields a wild match very close to what the author states; it is 62.7% real matches (I will not continually do the math again and again). Yes use the poisson distribution (which you did not recognize). Now how do we match up…our genome only compares segment for segment 62.7% of the time; it does not mean we compare 98.73% of the time. I let you go on without examining one of the major problems I brought up in the beginning; the 2.4 Gb/ 3.1Gb align able segments which you do not address. The absolute best claim the evolutions view could possibly make would be a 2.4/3.1 ~ 77% similarity. Also the additions of base pairs or subtraction of base pairs is not ethical in trying to have the genes come out to the same length. I pointed out the fact several times that there can be 6 separate coding of a single gene by altering the entry point in both directions; by adding one bp the coding losses its context (it is not the same gene).

“If the author had used 20BP instead he would have gotten another number (~72.7). If he'd used 50BP it would have been lower (~45.1). The only way to reconcile these basically arbitrary blocks is to bring them all back to the same scale.”

You better explain your reasoning here because I see no foundation for this. At minimum I need a citation (see if you can quantify it without making stuff up).

 

[Naraoia]

You better explain your reasoning here because I see no foundation for this. At minimum I need a citation (see if you can quantify it without making stuff up).

I suggest you generate some manageable-sized DNA strings and try...

 

[Blayz]

A comparison of 98.73% bp similarity yields a wild match very close to what the author states;

What does this even mean. What is "wild" about it, exactly?

it is 62.7% real matches

I'm not denying that the original metric generates a value of 62.7%.

Now how do we match up…our genome only compares segment for segment 62.7% of the time; it does not mean we compare 98.73% of the time.

They are measuring the same thing, with a different unit. It's like saying we are travelling at 50 miles/hr and not 80 km/hr, when they are effectively the same thing. 98.41 per 1BP is the same measurement as 62.7% per 30BP. It is saying exactly the same thing, just using different units.

I let you go on without examining one of the major problems I brought up in the beginning

You "let me" huh?

I have no intention of agreeing to your goalpost change. Let's settle argument 1 before moving to argument 2.

“If the author had used 20BP instead he would have gotten another number (~72.7). If he'd used 50BP it would have been lower (~45.1). The only way to reconcile these basically arbitrary blocks is to bring them all back to the same scale.”

You better explain your reasoning here because I see no foundation for this. At minimum I need a citation (see if you can quantify it without making stuff up).

It's simple math. If I have 62.7% of 30BP matches then i have 30throot of 0.627 (=0.9841) of 1BP matches, and then 0.9841^20 for 20BP matches and 0.9841^50 for 50BP matches.

I suggest you generate some manageable-sized DNA strings and try

A good idea. You could even download the human and chimp genomes from NCBI, and the perl script from the uncommon descent author. Said script contains a variable currently set to 30 which could be changed to 20 or 50.

EDIT: I'd do a simulation with a higher sample rate that generates 300-400 million sequences, then map with bowtie, but I am guessing Zaius doesn't have access to a decent 64bit linux machine.

 

[Zaius137]

Confessions of a closet evolutionist.

When I first started my education I dreamed of being an eminent evolutionist. Studying fossils and putting together the past from what science has discovered. I sought advice from school councilors and others. I remember visiting a respected instructor who seeing my grades only placed me in the low 2.0 range. I remember what he said to this day… He dashed my hopes in telling me I was overqualified to become an evolutionist. My friend looking over your math I must conclude we are overqualified to be evolutionists.

 

[Incariol]

Confessions of a closet evolutionist.

When I first started my education I dreamed of being an eminent evolutionist. Studying fossils and putting together the past from what science has discovered. I sought advice from school councilors and others. I remember visiting a respected instructor who seeing my grades only placed me in the low 2.0 range. I remember what he said to this day… He dashed my hopes in telling me I was overqualified to become an evolutionist. My friend looking over your math I must conclude we are overqualified to be evolutionists.

I'm not sure what this is, I think this is intended to be a joke, with "evolutionists" have an average GPA under 2.0, but there's not actually anything witty, funny or even remotely plausible in it.

 

[Zaius137]

You must be a Baptist…

 

[Blayz]

I'm not sure what this is, I think this is intended to be a joke, with "evolutionists" have an average GPA under 2.0, but there's not actually anything witty, funny or even remotely plausible in it.

Well I read it as "I no longer have a cogent rebuttal to your explanation, and am far to proud to admit to being wrong on this forum, so shall now post something irrelevant."

Oh, and to head of the obvious retort, here's me admitting to being wrong on CF just in 2011:

http://www.christianforums.com/t7573879-2/#post57933516
http://www.christianforums.com/t7541492-6/#post56921100

 

[Incariol]

You must be a Baptist…

Ummmm... no. I'm not. Where in the name of Torak would you get that impression?