Humans and chimps not 1% different?

[nbs2]

Now, I'm long since removed from my days of researching JAMA, NEJM, and Science to keep with with changes in the genetic analysis field.

From what I understand/vaguely remember, the idea that the two species are only 1% different was based on the genes that we have in common. It appears that Science is now willing/wanting to assert that there is a greater difference, as genetic expression and missing/extra DNA account for more than Wilson/King had considered.

Can someone clarify this so that I can discuss the topic (mildly) intelligently.

 

[pooky]

I'll give it a shot...

You are essentially correct about the 1% figure. They got this by lining up our genes, and finding that about 1% of them had small differences. Later, they lined up the sequence of the genes, and found slightly more (1.5% or so) differences, but still in the ballpark.

What this editorial is trying to say is that a) we are more than the sum of our differences, and that b) parts of the genome that were thought to do nothing might in fact do something.

Gene duplication is an example. If humans and chimps both have an identical gene that produces some product, but humans have 10 copies while chimps have only 1, this accounts for a 0% difference in DNA by the old measure (since the genes are identical) but a big difference in the potential amount of product produced.

Another example is gene regulation. Let's say (simplifying, of course) that gene A controls the development of arm bones in the embryo, and that humans and chimps have identical copies of gene A. But gene A needs a switch to tell it when to turn on and off. We'll call gene B the gene that turns gene A off. If the human copy of gene B mutates so that it gets turned off much earlier than in chimps, we get much shorter arms in humans (because the arms stop developing while the rest of the body grows). Here we have a small change in 1 gene that produces a huge change in the visible product. A lot of the structural differences in organisms are the results of these kinds of regulatory switches.

A third example is junk DNA. This is DNA between genes that doesn't code for any product. We used to think it did nothing, and so it wasn't figured into the 1% figure. Now it's looking like this isn't true anymore, and there are much bigger differences in this section of the genome. This stuff can change the shape of chromosomes and cause changes in the way working genes are regulated, it can move in situ and screw up working genes, and it can probably do lots of other things we have no idea about.

Hope that helps!

 

[twoodcc]

i'm not even gonna get into this, but i'm glad that some are finally starting to say that we are more than 1% different

 

[elfin buddy]

i'm not even gonna get into this, but i'm glad that some are finally starting to say that we are more than 1% different

Why does that make you glad? Were you insulted by the notion that we are similar to other primates?

 

[nbs2]

<wonderful, succinct, explanation>

Hope that helps!

Immensely. I think I had most of the basic concepts understood, but I couldn't explain them to myself - and therefore I don't think I really understood. Everything is much clearer now.

Why does that make you glad? Were you insulted by the notion that we are similar to other primates?

Likely political debate is why I almost started this in the PRSI forum.

But, between pooky's great explanation and the apparent knowledge that there were these slight differences even at the time of the original research, I'm disappointed that the 1% theory lasted so long. I wasn't around, let alone capable of understanding news events, but I imagine that the 1% theory garnered more attention than this rebuttal. But, we'll see how long people will continue to parrot the outdated assertion.

 

[aricher]

I for one will welcome our new monkey overlords.

US researchers get stem cells from cloned monkeys

 

[Abstract]

Hmmmm......I always thought we were more than 1% different from chimps. I would have thought at least 2.37% different. Maybe 2.41%.

 

[Mr Skills]

Hmmmm......I always thought we were more than 1% different from chimps. I would have thought at least 2.37% different. Maybe 2.41%.

2.37% maybe, but anything over 2.39% just smacks of human arrogance.

 

[xsedrinam]

Hmmmm......I always thought we were more than 1% different from chimps. I would have thought at least 2.37% different. Maybe 2.41%.

2.37% maybe, but anything over 2.39% just smacks of human arrogance.

Le'me get back to ya' on that one.

 

[jeo]

A lot of our recent revelations re: genetics and differential protein translation amongst individuals and species comes from a recent paper (Nature, May, 2007) from the ENCODE project (stands for Encyclopedia of DNA Elements) and pretty much blows away what we thought we knew about genetic diversity. Basically, in creating this encyclopedia, researchers have found that different products can be translated from splicing together components from a bunch of what were previously thought to be distinct genes, which is both bizarre and mind blowing. A lot of what we used to think of as 'junk' DNA is now being recognized as playing an important part in genetics!

 

[Don't panic]

But, between pooky's great explanation and the apparent knowledge that there were these slight differences even at the time of the original research, I'm disappointed that the 1% theory lasted so long. I wasn't around, let alone capable of understanding news events, but I imagine that the 1% theory garnered more attention than this rebuttal. But, we'll see how long people will continue to parrot the outdated assertion.

i am not sure how it makes much "qualitative" difference that there are changes in the levels of expression of genes in addition to the variation encoded directly in the primary DNA sequence.
It's obviously important mechanistically and from an evolutionary point of view, but it doesn't change much in term of how similar, or dissimilar we are from other species, certainly not at a philosophycal level.

in terms of expression profile, there are orders of magnitude of more differences between a human neuron and hepatocyte, than between a human and a mouse neuron.

In addition, one aspect missing (yet) in the analysis is the internal species variance: how dissimilar are these same additional levels of control within one species? whatever those quantities are in the two species being compared, it needs to be subtracted from the cross-species variance, because it constitutes the 'noise' of the system. And you'd be surprised on how high that 'noise' can be.

If anything, the realization that subtle differences in levels of expression, gene copy number, alternative splicing patterns, post-translational modifications, SNPs and so on lead to significant changes in phenotypes underlines even more how intrinsically similar to other living organisms, and how little 'special' we are.

imagine cooking a simple dish of pasta. you start with a few ingredients: a pot of boiling water, salt, pasta, olive oil, tomato sauce, hot peppers, garlic, cheese.
a basic starting recipe gives you a 'normal' serving of pasta with a mild sauce.
you have a machine that will randomly change the amount one of more of the variables, from cooking time to amount of salt , garlic, cheese and so on.
the machine generates 50 different varieties, and serve them to a large number of people. If one dish is appreciated, the machine continues to make it, if not it changes something or stops making that version.
After some time you certainly will have likely eliminated the "unedible" variants (uncooked, gooey, tons of salt, super-garlicky), and depending on the preferences of the people in the room 'selected' a few preferred varieties: basic tomato sauce, spicy tomato sauce, cheese, oil and garlic, and so on.

The ingredients are the same, but different amounts and the way they are combined lead to different results. but at the end of the day it still is pasta.

 

[Eric Piercey]

i'm not even gonna get into this, but i'm glad that some are finally starting to say that we are more than 1% different

Yeh we're way superior to those filthy animals. We can destroy planets.

edit- I apologize if you didn't mean it that way, that's was how I read it. For all I know you're a geneticist and you were outraged the scientific community hadn't embraced a 2.3% difference, or somthing.

 

[Jedi128]

imagine cooking a simple dish of pasta. you start with a few ingredients: a pot of boiling water, salt, pasta, olive oil, tomato sauce, hot peppers, garlic, cheese.
a basic starting recipe gives you a 'normal' serving of pasta with a mild sauce.
you have a machine that will randomly change the amount one of more of the variables, from cooking time to amount of salt , garlic, cheese and so on.
the machine generates 50 different varieties, and serve them to a large number of people. If one dish is appreciated, the machine continues to make it, if not it changes something or stops making that version.
After some time you certainly will have likely eliminated the "unedible" variants (uncooked, gooey, tons of salt, super-garlicky), and depending on the preferences of the people in the room 'selected' a few preferred varieties: basic tomato sauce, spicy tomato sauce, cheese, oil and garlic, and so on.

The ingredients are the same, but different amounts and the way they are combined lead to different results. but at the end of the day it still is pasta.

I really like this pasta example of genetics. What a great metaphor. It's such a simple way of explaining how life works.

Oh and I don't really understand the happiness about being more than 1% different than other animals. What I find comforting about this information is that "junk DNA" finally has a use. That was what always bothered me. How could so much DNA just be completely useless....

 

[Xfujinon]

In regards to the above poster, in all likelihood the DNA is NOT worthless, we simply lack a comprehensive understanding of what it may do. What is mind-blowing to me is the very real possibility that we may not even have a theoretical construct that fits what it might do. Sort of like what a Neanderthal would think if he saw a bicycle; you are missing too much information (conceptual and practical) to really appreciate what one is looking at.

I do research in immunology. Even the most basic immunologic science boggles my mind at times. Every time our lab manages to coax out something new, it makes the picture even more complex (but beautiful, in a way).

I would bet that there are not too many overt differences in the line-by-line genetic code between primate genera; I will postulate, however, that there are many radical differences in regard to post-transcriptional or post-translational modifications of the RNA or gene products based on those genes. And, as the brilliant pasta example above indicates, probably an even more bizarre array of combinatorial differences in the post-translationally modified products too!

Keep reading. The field will only become more fascinating.

 

[pooky]

I would bet that there are not too many overt differences in the line-by-line genetic code between primate genera; I will postulate, however, that there are many radical differences in regard to post-transcriptional or post-translational modifications of the RNA or gene products based on those genes.

That would be a good bet. I read somewhere (and of course, I can't for the life of me remember where) that there is more raw genetic diversity between individual chimps than there are differences between humans and chimps. That is to say, humans and chimps might be only 1% different, but any one chimp might be 2 or 3% different from any other chimp! By comparison, the human species is very low on diversity.

Of course, the existence of such morphological uniformity within chimps despite all of that genetic diversity, and the existence of such morphological and functional differences between humans and chimps (much more than our "1%" might imply) should immediately suggest that perhaps our simple quantitative measurements of genetic diversity don't really translate all that well to functional morphology. To put it another way, what matters is not how different you are, but what those differences are. Seems perfectly logical when you think about it.

 

[Pani]

Personally, I like the bonobos better! They are a female dominated primate species. They are also peaceful! Guess we don't have too much DNA in common!

 

[*Y*]

I think what the poster meant about being happy that we are more than 1% different is that it proves the whole evolution theory somehow wrong. Although that is just my take on things.

 

[Don't panic]

I think what the poster meant about being happy that we are more than 1% different is that it proves the whole evolution theory somehow wrong. Although that is just my take on things.

????
why would you think that? it obviously doesn't change an iota: whether the changes are 1% or a little bit more, and the fact there the situation is more complex than just changes in the primary sequence of coding regions, doesn't affect the fact that we do share common ancestors with primates and they are by far our closest relatives.

i must add that we are at a point where evolution is a pretty much established fact and in its major tenets simply cannot be 'proven wrong'.
some minor aspects of it, particular mechanisms, or interpretation of data will change of course, but as far as the 'core' parts, we are way beyond the prove/disprove stage.

 

[MarkCollette]

A lot of what we used to think of as 'junk' DNA is now being recognized as playing an important part in genetics!

What I find comforting about this information is that "junk DNA" finally has a use. That was what always bothered me. How could so much DNA just be completely useless....

I am by no means a biologist, but I always thought it was kind of crazy, that the concept of "junk DNA" came about, especially at a time when we knew that we didn't know much about our DNA.

As a computer programmer, it always seemed to me like when a junior guy looks at a large mature code base, and doesn't really understand it, so they say that most of it is unnecessary.

 

[topicolo]

I am by no means a biologist, but I always thought it was kind of crazy, that the concept of "junk DNA" came about, especially at a time when we knew that we didn't know much about our DNA.

As a computer programmer, it always seemed to me like when a junior guy looks at a large mature code base, and doesn't really understand it, so they say that most of it is unnecessary.

It's a little different from programming. Most junk DNA are composed of a single sequence replicated hundreds to thousands of times and usually condensed so that their sequences can't be read by transcription enzymes to form proteins. If you were to use programming as an analogy, the DNA originally labelled as junk would appear to be the same code copied and pasted hundreds to thousands of times over and over and the entire section would be commented out.

That's why scientists originally thought the stuff was useless

 

[MarkCollette]

It's a little different from programming. Most junk DNA are composed of a single sequence replicated hundreds to thousands of times and usually condensed so that their sequences can't be read by transcription enzymes to form proteins.

If you were to use programming as an analogy, the DNA originally labelled as junk would appear to be the same code copied and pasted hundreds to thousands of times over and over and the entire section would be commented out.

Just to prove I'm a nit-picky pain, the commented out code would definitely not end up in the final program, whereas "junk DNA" is still there, it just "can't be read", which to me would definitely not lead me to call it "junk", but would make me reevaluate if we fully understand how things can be read.

 

[Don't panic]

Just to prove I'm a nit-picky pain, the commented out code would definitely not end up in the final program, whereas "junk DNA" is still there, it just "can't be read", which to me would definitely not lead me to call it "junk", but would make me reevaluate if we fully understand how things can be read.

to stay with your analogy, the point is that we are not the "final program" either.
we are work in progress.
give it an additional few hundred of thousands of years of evolution and the current 'junk' will be changed/edit out or, if it is functional, not.
of course other novel additional junk could also be put in to be 'tested' in the lab of time.

not all the junk in the junkyard is junk, but most of the junk in the junkyard is junk. how do you sort the non-junk-junk from the junk-junk in the junkyard if you don't know how to distinguish the non-junk-junk from the junk-junk?

 

[topicolo]

Just to prove I'm a nit-picky pain, the commented out code would definitely not end up in the final program, whereas "junk DNA" is still there, it just "can't be read", which to me would definitely not lead me to call it "junk", but would make me reevaluate if we fully understand how things can be read.

Commented code would not end up in a compiled program, but DNA isn't the equivalent of a compiled program. The "final program" is the myriad of proteins and RNA that interact with each other inside and outside the cells that keep us going. The DNA is the source code only and does nothing by itself unless it is "compiled" by DNA transcriptases, topoisomerases, promoters, etc. so the analogy still stands.

 

[Iscariot]

i'm not even gonna get into this, but i'm glad that some are finally starting to say that we are more than 1% different

You Maniacs! You blew it up! Ah, damn you! God damn you all to hell!

 

[Fiveos22]

Well played AhmedFaisal, Don't Panic, Topicolo, and Pooky.

Just to toss my 2 cents in there:

A great example of the order of complexity that we are beginning to appreciated in Genetics can be seen by examining the genetic underpinnings of Prader-Willi and Angelman syndromes. [light reading] One of the gene complexes that regulates the genetic imprinting in those syndromes, SNURF-SNRPN, has over 100 exons that can be alternatively spliced and have sense complement strands...!

In English: Imagine that I wrote an essay 100 sentences long. Now imagine that the sentences can be reordered hundreds if not thousands of ways and still make sense. Now imagine that this essay could be read backwards (letter for letter), sentences shuffled, and it would still make sense. I don't know about you, but my mind would be blown by that essay.

But apparently we are finding that that magnitude of complexity exists in the genomes of many organisms. Actual number of basepair differences seem insignificant to changes on that scale.