i need a help about understanding evolution

[Essay]

Essay

english is not my first language.. so Iam somekind didnt understand what you wrote

i hope you write what you want to say in few points

please use simple uk english words

and thanks

 

You found different percent numbers, because you were reading about different kinds of similarity.

===

 

 

In the first link from your OP, they talk about two kinds of similarity: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2049197/

"Despite an overall sequence identity between human and chimpanzee genomic coding regions of 98%–99%, we observe that 6%–8% of surveyed alternative exons display pronounced splicing level differences."

...where they describe "overall sequence" and "alternative exons" as having different percentages.

 

 

So while they agree that "overall" (for the coding regions!!!) chimps and humans are "98%-99%" identical,

there are many other ways to look at the genome, such as the non-coding regions, or the "alternative exons," which they mention, or the introns, or the InDels, or the transposons, etc., within the genome.

With these different ways to compare the similarity between chimps and humans, there seem to be more differences.

===

 

 

Where they say:

"Our results thus provide evidence that alternative splicing changes have evolved rapidly and in parallel with changes in transcriptional regulation, affecting an additional set of genes and associated gene functions. The identification of alternative splicing differences between humans and chimpanzees provides a new basis for understanding the molecular mechanisms underlying the evolution of primate species-specific characteristics."

They point out two different ways ("alternative splicing" & "transcriptional regulation") that the same genes can be rearranged and made to work differently.

 

...like two books could have 98% the same words, but if the words are arranged differently, then each book would tell a different story.

===

 

But I can see why, if you don't fully understand the context for these percentages you find in different articles, that it would be hard to see why the numbers are different.

 

Feel free to keep asking, if something is confusing, especially if you find a specific question or possible contradiction.

 

~

[james bond]

 

You found different percent numbers, because you were reading about different kinds of similarity.

===

 

 

In the first link from your OP, they talk about two kinds of similarity: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2049197/

...where they describe "overall sequence" and "alternative exons" as having different percentages.

 

 

So while they agree that "overall" (for the coding regions!!!) chimps and humans are "98%-99%" identical,

there are many other ways to look at the genome, such as the non-coding regions, or the "alternative exons," which they mention, or the introns, or the InDels, or the transposons, etc., within the genome.

With these different ways to compare the similarity between chimps and humans, there seem to be more differences.

===

 

 

Where they say:

They point out two different ways ("alternative splicing" & "transcriptional regulation") that the same genes can be rearranged and made to work differently.

 

...like two books could have 98% the same words, but if the words are arranged differently, then each book would tell a different story.

===

 

But I can see why, if you don't fully understand the context for these percentages you find in different articles, that it would be hard to see why the numbers are different.

 

Feel free to keep asking, if something is confusing, especially if you find a specific question or possible contradiction.

 

~

 

thanks .. i got it now

i want to know .. what is the non-coding regions ??

i hope you help me with rest of my quotes

 

[Essay]

thanks .. i got it now

i want to know .. what is the non-coding regions ??

i hope you help me with rest of my quotes

 

Thanks, though I'm no expert, and my knowledge is fairly outdated. But from what I gather, in very simple language....

 

"non-coding regions" have genes that modify how the 'coding' genes work.

 

In other words....

Even if (within any given cell) the coding genes are very similar between chimps and humans,

during development the coding genes are then modified (by the non-coding parts of DNA),

which changes how the coding genes express ...in phenotype.

===

 

I had also looked briefly at the HAR1 link, which was about something called the Human Accelerated Region! Wow, that still sounds very interesting, and I may follow up if nobody else does. There seem to be lots of good search results, including wikipedia at the top, when I type in: Genetics HAR1.

 

Almost a decade ago I read about a newly discovered genetic mechanism, for helping promote more of a certain kind of localized and "favorable" mutation, that was found only in humans (and one other primate iirc), and I wonder if this is the same thing. It involved genes in a local region of our genome associated with digestion, so it made sense, since our diets have continued changing so radically over the past 5-10 thousand years. And interestingly, certain genes associated with autism are located in the same region as these digestive genes (or might even be the same 'digestive' genes, but also used later in development during brain formation), which could help explain some things about autism, but which would also be an example of one possible "non-coding" modification.

===

 

But just the fact that there is something called the Human Accelerated Region, which applies to those "98% the same" genes,

should show how we can now be very different from chimps,

even starting with the same basic toolbox, or artist's palette, of genes.

 

~

[james bond]

 

Thanks, though I'm no expert, and my knowledge is fairly outdated. But from what I gather, in very simple language....

 

"non-coding regions" have genes that modify how the 'coding' genes work.

 

In other words....

Even if (within any given cell) the coding genes are very similar between chimps and humans,

during development the coding genes are then modified (by the non-coding parts of DNA),

which changes how the coding genes express ...in phenotype.

===

 

I had also looked briefly at the HAR1 link, which was about something called the Human Accelerated Region! Wow, that still sounds very interesting, and I may follow up if nobody else does. There seem to be lots of good search results, including wikipedia at the top, when I type in: Genetics HAR1.

 

Almost a decade ago I read about a newly discovered genetic mechanism, for helping promote more of a certain kind of localized and "favorable" mutation, that was found only in humans (and one other primate iirc), and I wonder if this is the same thing. It involved genes in a local region of our genome associated with digestion, so it made sense, since our diets have continued changing so radically over the past 5-10 thousand years. And interestingly, certain genes associated with autism are located in the same region as these digestive genes (or might even be the same 'digestive' genes, but also used later in development during brain formation), which could help explain some things about autism, but which would also be an example of one possible "non-coding" modification.

===

 

But just the fact that there is something called the Human Accelerated Region, which applies to those "98% the same" genes,

should show how we can now be very different from chimps,

even starting with the same basic toolbox, or artist's palette, of genes.

 

~

thanks

 

how can mutations make us evolve if asingle mutation take that time ?

 

In a paper for DURRETT R, SCHMIDT D, which was published in 2007 in the journal Genetics in order to reach conclusions about the theory of the average time required to install the mutations within the total population of the kind of neighborhoods through calculations and computer simulation models.

DURRETT, SCHMIDT found that the period of time necessary to install only a single mutation in the ancestral primate is six million years. And getting only two mutations Thbytha through Darwinian evolution "for humans is 100 million years old."

https://www.sciencemag.org/content/316/5833/1836.summary

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581952/

[CharonY]

The second paper, which is unrelated to the first (which is a science news article) refers to a specific question. What is the time frame to have one binding site for a regulatory protein vanish and a new one rise. This is not about getting and fixing two mutations arbitrary mutations. The authors calculate a number of scenarios including types of selection. What they find specifically for humans is that the rise of a new binding sites takes about 60k years but that a coordinated mutation (one turning on and one turning off a binding site) is unlikely to occur (because of the long time frame needed).

 

The quote does not really accurately reflect the paper and all (and cites the wrong year). Which I presume is source of the misunderstanding. It also should be noted that the paper specifically argues against errors of intelligent design proponents, which makes it even worse to misquote them.

[james bond]

The second paper, which is unrelated to the first (which is a science news article) refers to a specific question. What is the time frame to have one binding site for a regulatory protein vanish and a new one rise. This is not about getting and fixing two mutations arbitrary mutations. The authors calculate a number of scenarios including types of selection. What they find specifically for humans is that the rise of a new binding sites takes about 60k years but that a coordinated mutation (one turning on and one turning off a binding site) is unlikely to occur (because of the long time frame needed).

 

The quote does not really accurately reflect the paper and all (and cites the wrong year). Which I presume is source of the misunderstanding. It also should be noted that the paper specifically argues against errors of intelligent design proponents, which makes it even worse to misquote them.

thanks

How is the similarity calculation here?

 

here..Chimpanzees are 96% to 98% similar to humans

http://genome.wellcome.ac.uk/doc_WTD020730.html

 

here.. Similarity between human and mouse is 75%

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.100

 

here.. Similarity between human and mouse is 90%

http://www.genome.gov/page.cfm?pageID=10005831

 

here.. Similarity between human and mouse is 99%

http://www.nature.com/nature/journal/v420/n6915/full/420509a.html

==================

i need to know how they calculate the similarity !!

why in human is 98 .. the mouse is 99

how they calculate similarity in each link !!

[Finding the Elephant]

Does this mean we evolved from mice or that mice evolved from us?

[Fuzzwood]

Neither. It's just that we all have some machinery in common like our senses, respiratory and digestive system. We also have the same general body shape.

[delboy]

Does this mean we evolved from mice or that mice evolved from us?

We both evolved from a common ancestor which existed very roughly something like 80-100 million years ago (it's probably known more accurately). So a species existed then that was neither mouse nor human. It became divided and evolved into 2 species. One of those evolutionary lines eventually led to mice and one to humans. So the genetic changes that happened along each of those lines accounts for the differences, having started at an identical point. Which is why the genetic differences between us and chimpanzees is much less since our common ancestor with them existed only 6 million years ago.

[CharonY]

 

thanks

How is the similarity calculation here?

 

here..Chimpanzees are 96% to 98% similar to humans

http://genome.wellcome.ac.uk/doc_WTD020730.html

 

here.. Similarity between human and mouse is 75%

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.100

 

here.. Similarity between human and mouse is 90%

http://www.genome.gov/page.cfm?pageID=10005831

 

here.. Similarity between human and mouse is 99%

http://www.nature.com/nature/journal/v420/n6915/full/420509a.html

==================

i need to know how they calculate the similarity !!

why in human is 98 .. the mouse is 99

how they calculate similarity in each link !!

 

 

It depends on what you calculate and it depends on what you want to talk about. Most mammals have the same functional genes. The reason is that we have the same basic physiology. However, while the genes are very similar to each other, they will have sequence differences.

 

Alternative estimates are based on actual sequence similarities. Here again several possibilities for comparisons exist and each have their own relevance in specific contexts.

One could look at sequence divergence in well conserved genes. Here you get a conservative estimate of divergence as many mutations in those genes would likely be selected against. This is what has been used mostly in the past as it was too costly to sequence whole genomes.

You can also compare align all identified genes, instead of selected ones which will show more divergence. Or you can also try to look at non-coding regions, which will have a much higher mutation rate. It would also make a difference whether you look at the cDNA level or on the raw sequence (containing introns). Or you could look at divergence on the amino acid level. You could also include intergenic regions which are more variable (as they do not code for proteins). Or you could look at differences in the gene order and see if they are similar. Your link actually express similarities in various ways if you read them carefully.

 

Each of these measures are relevant in different contexts and used for different models.

[Strange]

i need to know how they calculate the similarity !!

 

Then you will need to study biology.

 

why in human is 98 .. the mouse is 99

 

Because they are measuring similarity in different ways.

[Essay]

here.. Similarity between human and mouse is 90%

http://www.genome.gov/page.cfm?pageID=10005831

 

here.. Similarity between human and mouse is 99%

http://www.nature.com/nature/journal/v420/n6915/full/420509a.html

==================

i need to know how they calculate the similarity !!

....

how they calculate similarity in each link !!

The difference, or "how they calculate the similarity," is explained in the link that the number is quoted from. Reading more of the text will help you learn more English, as well as Biology! Quoting the text, which the number comes from, will make answers easier to find; instead of just repeating, "Similarity between human and mouse is xx%," and then typing in those different numbers you find.

===

 

In the 'genome' link, they explain how "...more than 90 percent of the mouse genome could be lined up with a region on the human genome. That is because the gene order in the two genomes is often preserved over large stretches, called conserved synteny."

 

In the 'nature' link, they explain how their study “...reveals about 30,000 genes, with 99% having direct counterparts in humans.”

 

But just because they do find "direct counterparts" across the two genomes, that doesn't also mean they find the same "conserved synteny," or that the "gene order" will be calculated to be similar. Right?

===

 

As the first link points out:

"...the mouse genome could be parsed into some 350 segments, or chapters for which there is a corresponding chapter in the human genome.”

"Although virtually all of the human and mouse sequence can be aligned at the level of large chapters, only 40 percent of the mouse and the human sequences can be lined up at the level of sentences and words."

 

So from that perspective you might say they are only 40% similar; right?

===

 

And as the second link mentions:

"Humans appear to have about the same number of genes, with similar sequence, and we both like cheese. So why aren't mice more like us? The answer probably lies in the regulation of those genes."

 

It seems, between various differences in sequence and regulation, the same dictionary of genes can be used to build very different books.

===

 

When science looks "at the level sentences and words," then the percentages are calculated as less similar; but

 

when science looks at the level of the book, "or chapters," then the percentages are calculated as more similar.

 

~