Chimps and humans: How similar are we really?

[sfs]

We have recently found 1,307 orphan genes that are completely different between humans and chimpanzees, and these from just four areas of tissue samples. We can only imagine the vast numbers of differences that will be revealed once more areas of the anatomy and physiology are analyzed (see J. Ruiz-Orera, 2015, “Origins of De Novo Genes in Humans and Chimpanzees”, PLoS Genetics. 11 (12): e1005721)

Or we could read the paper and discover that the great majority of these novel "genes" are not translated into peptides and are very likely not functional ("the majority of these transcripts do not encode functional proteins"). The researchers actually found protein produced by one orphan human gene, and any evidence for translation in 6 of them. For those genes, they found evidence of purifying selection (i.e. they probably are functional); for the others, the great majority, they didn't. Why didn't you mention these conclusions of the paper?

Any thoughts?

Just a question: did you read the paper?

 

[sfs]

Actually a complete genome comparison of human and chimp DNA has never been done (period)! However the masses are given this impression (the art of persuasion) and the details are not clarified.

The very best and most complete study so far (Fujiyama, A., Watanabe, H., Toyoda, A., Taylor, T.D., Itoh, T., Tsai, S.F., Park, H.S., Yaspo, M.L., Lehrach, H., Chen, Z., Fu, G., Saitou, N., Osoegawa, K., de Jong, P.J., Suto, Y., Hattori, M., and Sakaki, Y. 2002. ‘Construction and analysis of a Human-Chimpanzee Comparative Clone Map.’ Science 295:131-134) only utilized 19.8 million base pairs.

You're a wee bit behind the times. The chimpanzee genome was sequenced and compared to the human genome in 2005. A total of 2.7 billion base pairs of chimpanzee sequence could be compared.

Now then, when speaking of the “genome” we are speaking of much more than just the recorded sequencing of DNA in a given or comparative species

No, that's exactly what we mean (assuming I can understand what you're saying here).

(which again has never actually been done).

It's been done for the euchromatic genome for many species.

The Human Haploid Genome contains around 3 BILLION base pairs. Now take away the approximate 2,010,000,000 similar pairs (around 67%), that leaves 990,000,000 base pairs of which 1/6th vary which means there may be around 165,000,000 differences in the base pairs between humans and chimps. That is just one of the ways this figure has been derived. Another straight forward comparison shows there to be 120,000,000 base pairs as differing (4% of 3,000,000,000). Again, despite the rhetorical manipulations which make us think we are almost the same, that is a huge number of differences (especially considering THE FACT that we do not understand the purpose and function of but a few % of the genome itself…see the Encode Project).

Any two humans differ by about 10 million base pairs, which is also a lot. So?

As for the near 67% of the DNA of all species categorized “Primate” as appearing to be nearly identical (most of which translates into our having blood vessels, skin, a heart pump, a brain and so on), this does not mean one came from the other….but based on the way we have determined to categorize things this really only means we are all in that man-determined category and nothing else! Via this section. we all are mammals, with hair, and genitalia, feeding our young via mammary glands, and so on and within that all primates. The approximated “5% difference” exists only in the other 33% which means we have an actual difference of about 1/6th of what makes us human as opposed to ape, and that number of differences in the base pairs is still in the millions of differences (most of which we do not even understand at this point, though we are coming along).

I have no idea what this division into 67% and 33% means. It corresponds to no division in the genome that I've ever heard of. Differences between humans and chimpanzees (and between individual humans) are scattered throughout the genome.

Why not just say we have found at least 120,000,000 differences?

What we actually said: "a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor . . . constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements."

Secondly, some wouldn’t the 2nd law of genetics tell us that recessive traits (such as our more ancient ape traits) not only repeat themselves in future generations, but on occasion actually revert? Wouldn’t we see examples in our species instances when the qualities and characteristics or the recessives re-present themselves and occasionally take over?

The confusion about genetics here is so deep that I'm not going to attempt to plumb it.

 

[pshun2404]

You're a wee bit behind the times. The chimpanzee genome was sequenced and compared to the human genome in 2005. A total of 2.7 billion base pairs of chimpanzee sequence could be compared.

Please give me a reference for this so I can check it out, thanks.

Differences between humans and chimpanzees (and between individual humans) are scattered throughout the genome.

Yes I know but that is not the impression given to the common person or most students.

"a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor . . . constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements."

Differences are not the same as changes. They claim 35,000,000 "changes" but that is simply what the "scientists" infer who accept the hypothesis (not the science itself). The Science merely tells us they are there and the scientists are telling us what they think it means (not the same...one is true the other conjecture). Even insertion/deletion is somewhat persuasive language (especially when espoused by someone representing authority). We call it insertion but do we have have less developed humans without them and now with them? Same with "deletions". Do we have examples that humans use to normally have these and now they are gone?

The confusion about genetics here is so deep that I'm not going to attempt to plumb it.

Not confused at all I merely generalized for the readers who have less knowledge of genetics. The law of independent assortment later gives rise to the generalization I referred to. Of course reliability of this is most useful in predicting inheritance of some diseases but it applies none the less.

 

[pshun2404]

please give me a link of something...thanks

 

[PsychoSarah]

Secondly, some wouldn’t the 2nd law of genetics tell us that recessive traits (such as our more ancient ape traits) not only repeat themselves in future generations, but on occasion actually revert? Wouldn’t we see examples in our species instances when the qualities and characteristics or the recessives re-present themselves and occasionally take over?

Uh, genetics is a huge component of my major. There is no "second law of genetics", recessive traits are called such because they aren't usually expressed when a person's genome also contains another, more dominant allele (variant of a gene, such as how blue eyes are a recessive trait to brown eyes in most instances). They are passed down to future generations and it is not uncommon for individuals farther down the line to eventually express these traits (which is part of why hemophilia would never cease to be in the human population thanks to natural selection, even if we never treated it), but I would never refer to this as reverting. If you are actually talking about ancestral traits reappearing in a small number of people, such as the presence of tails, that actually does happen on rare occasions. Here's a picture http://cdn2.gbtimes.com/cdn/farfutu...6103531f107dt20140424213608.jpg?itok=PLUQCUMD and in case it wasn't obviously implied, the image does contain unblurred baby butt so you can see the tail.

 

[sfs]

You're a wee bit behind the times. The chimpanzee genome was sequenced and compared to the human genome in 2005. A total of 2.7 billion base pairs of chimpanzee sequence could be compared.

Please give me a reference for this so I can check it out, thanks.

Initial sequence of the chimpanzee genome and comparison with the human genome

Differences between humans and chimpanzees (and between individual humans) are scattered throughout the genome.

Yes I know but that is not the impression given to the common person or most students.

Where have you seen it suggested that the differences were grouped together? What is your source for the 33%/67% breakdown you mentioned?

"a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor . . . constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements."

Differences are not the same as changes. They claim 35,000,000 "changes" but that is simply what the "scientists" infer who accept the hypothesis (not the science itself). The Science merely tells us they are there and the scientists are telling us what they think it means (not the same...one is true the other conjecture).

No. Just no. Scientific conclusions are just as much a part of science as data. You're treating data as if it were the entirety of science, which isn't the case at all. In fact, uninterpreted data doesn't mean anything. If you reject scientific inference, then no, these aren't change, but they're also not differences between species. They're not measurements of DNA at all; they're just dots in a capillary tube in a machine filled with liquids. The whole point of science is to draw conclusions about how the natural world works. And one of the conclusions science came to a long time ago is that humans and chimpanzees are related.

Even insertion/deletion is somewhat persuasive language (especially when espoused by someone representing authority).

Again, no. The language is not "persuasive": it's not intended to persuade anyone that humans and chimpanzees are related. Frankly, the authors are not addressing a paper like this to anyone who would doubt that fact. They're addressing it to other scientists.

We call it insertion but do we have have less developed humans without them and now with them? Same with "deletions". Do we have examples that humans use to normally have these and now they are gone?

How could we have that?

The confusion about genetics here is so deep that I'm not going to attempt to plumb it.

Not confused at all I merely generalized for the readers who have less knowledge of genetics.

What you wrote wasn't a generalization; it was wrong. "Ancient ape traits" have nothing to do with traits being recessive or dominant. Beyond that, I can't even figure out what you're trying to say. What does it mean for a recessive trait to 'revert'?

ETA: I'd still like to know whether you read the paper you cited in the OP.

 

[pshun2404]

Uh, genetics is a huge component of my major. There is no "second law of genetics", recessive traits are called such because they aren't usually expressed when a person's genome also contains another, more dominant allele (variant of a gene, such as how blue eyes are a recessive trait to brown eyes in most instances). They are passed down to future generations and it is not uncommon for individuals farther down the line to eventually express these traits (which is part of why hemophilia would never cease to be in the human population thanks to natural selection, even if we never treated it), but I would never refer to this as reverting. If you are actually talking about ancestral traits reappearing in a small number of people, such as the presence of tails, that actually does happen on rare occasions. Here's a picture http://cdn2.gbtimes.com/cdn/farfutu...6103531f107dt20140424213608.jpg?itok=PLUQCUMD and in case it wasn't obviously implied, the image does contain unblurred baby butt so you can see the tail.

Thanks Sarah...poor wording on my part....

 

[pshun2404]

Initial sequence of the chimpanzee genome and comparison with the human genome

ETA: I'd still like to know whether you read the paper you cited in the OP.

Yes I did, and the paper you sited above was amazing thanks...up until now I thought the 2,400,000,000 base pair sequences of the Encode Project were the most complete (for humans) and had no idea of this massive undertaking for the chimpanzee (can't read everything...I study in multiple areas of interest)...to get more out of it I will re-read it.

 

[PsychoSarah]

Yes I did, and the paper you sited above was amazing thanks...up until now I thought the 2,400,000,000 base pair sequences of the Encode Project were the most complete (for humans) and had no idea of this massive undertaking for the chimpanzee (can't read everything...I study in multiple areas of interest)...to get more out of it I will re-read it.

This site is a bit old, but it is a great tool for comparing gene sequences of various organisms and people from different regions of the globe http://www.bioservers.org/bioserver/ If you are interested, I will gladly type up directions on how to use it, or you can take the initiative as the site tells you how to use it as well. You do not need to register to use it, but you do if you want your progress saved. Note that it deals with mitochondrial DNA.

 

[sfs]

Yes I did

So if you had read the paper when you wrote the OP, why did you describe these orphan genes as if they were functional?

 

[Loudmouth]

Wong. K., “Tiny Genetic Differences between Humans and Other Primates Pervade the Genome”, Scientific American, Sept. 2014, reveals that the “…tiny portion of unshared DNA makes a world of difference: it gives us, for instance, our bipedal stance and the ability to plan missions to Mars. Scientists do not yet know how most of the DNA that is uniquely ours affects gene function.” And though the recent comparisons are performed on only about 33% of the genome, “individual differences pervade the genome, affecting each of our chromosomes in numerous ways.”

Which casts zero doubt on the reported sequence differences between the species.

So first I see language of persuasion! For example, IMWO the “only 1.8% difference” language describing the similarity between humans and chimps is just an opinion!

It is an observed fact.

"Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements."
http://www.nature.com/nature/journal/v437/n7055/full/nature04072.html

Do you know how to do math? Your opening post points to differences totaling less than 0.1% of the genome. You claim that these differences disprove the claim that the two genomes are 2% different. Do you see a problem with your math?

As you seemed to have discovered, more than 90% of the chimp and human genome has been compared. There is no reason to think that the remaining 10% of each genome is going to be drastically different from the other 90%, so the ~2% stands.

As for indels, they are considered a single mutation because the chances of 10 single base indels occurring right next to each other is much, much, much less probable than a single 10 base genome happening once. We also observe multi-base indels happening in real time in the human genome, so we do know that they happen. Can you give us a single reason why a 10 base gap should not be considered a single indel mutation instead of 10 independent one base indels that just happened to occur right next to each other?

 

[Loudmouth]

So if you had read the paper when you wrote the OP, why did you describe these orphan genes as if they were functional?

Perhaps he was using the ENCODE definition of functional?

 

[Papias]

A pity that this thread died.

It looks like it died because the reason for it to exist was addressed.

1. pshun started it suggesting that there are isn't that much similarity between chimps and humans, which his later posts show was because he doesn't accept their common ancestry.
2. tons of evidence was presented showing their very close commonality, and their clear common ancestry, including links to the peer-reviewed papers.
3. pshun gave up and left.

Your last post very much captured this history by asking "what's the point of all this?". It looks like the point was pshun denying our common ancestry with chimps, as he stated. That's well established, so the thread died.

So I guess I'm not sure what else you are looking for.

In Christ-

Papias

 

[pshun2404]

It looks like it died because the reason for it to exist was addressed.

1. pshun started it suggesting that there are isn't that much similarity between chimps and humans, which his later posts show was because he doesn't accept their common ancestry.
2. tons of evidence was presented showing their very close commonality, and their clear common ancestry, including links to the peer-reviewed papers.
3. pshun gave up and left.

Your last post very much captured this history by asking "what's the point of all this?". It looks like the point was pshun denying our common ancestry with chimps, as he stated. That's well established, so the thread died.

So I guess I'm not sure what else you are looking for.

In Christ-

Papias

Not really, I am still here watching others...and yes while I do believe each creature exhibits common descent within their own species I do not believe we share one lineage.

 

[juvenissun]

We have recently found 1,307 orphan genes that are completely different between humans and chimpanzees, and these from just four areas of tissue samples. We can only imagine the vast numbers of differences that will be revealed once more areas of the anatomy and physiology are analyzed (see J. Ruiz-Orera, 2015, “Origins of De Novo Genes in Humans and Chimpanzees”, PLoS Genetics. 11 (12): e1005721)


Orphan genes, as many here know, are found only particular lineages of creature or sometimes only in a specific species or variety within a species. What is really interesting is they appear to have no evolutionary history. Despite that we have come to know these genes are incredibly important! Their expression often dictates very specific qualities and processes allowing for specialized adaptations of particular tissues, like the antisense gene, NCYM, which is over-expressed in neuroblastoma; this gene inhibits the activity of glycogen synthase kinase 3β (GSK3β), which targets NMYC for degradation (Suenaga Y, Islam SMR, Alagu J, Kaneko Y, Kato M, et al. (2014) NCYM, a Cis-antisense gene of MYCN, encodes a de novo evolved protein that inhibits GSK3β resulting in the stabilization of MYCN in human neuroblastomas. PLoS Genet 10: e1003996. doi: 10.1371/journal.pgen.1003996). Some contribute to specific proteins unique only to that species or to varieties within a species.


This genetic curiosity has been being studied for around 20 years with little insight as to why they are there at all (where did they come from), and we are just beginning to see how they function, but the doubted thousands of additional differences this will add to the human/chimp difference scenario is staggering.


Any thoughts?

Go to a zoo and take a look of those animals.
Then one would clearly know how much differences are there.

This is simple hard fact. Why can't people see that? Even there is only 10E-100 genetic differences, that would be a very very significant differences. Genetic scientists should really ask themselves: why is that? Science is not able to answer this question.

 

[pshun2404]

And of course we share many anatomical similarities as we do with many primates. For example arms were a good idea what ever we need them for and yes we need triceps and biceps and so on to use them...big deal that does not make them our long lost cousins.

 

[pitabread]

Go to a zoo and take a look of those animals.
Then one would clearly know how much differences are there.

Biologists' methods of comparing species: detailed morphological/anatomical studies, developmental biology, complete genomic sequencing

Creationist method: "Hey guys, go visit the zoo!"

It's rather embarrassing...

 

[juvenissun]

Biologists' methods of comparing species: detailed morphological/anatomical studies, developmental biology, complete genomic sequencing

Creationist method: "Hey guys, go visit the zoo!"

It's rather embarrassing...

Biologists should be embarrassed. Spent so much money and so much energy and still can not ask the right question which a child can easily answer.

 

[pshun2404]

There are many similarities between these two species of that I do not doubt but the popularized "only about 1.8% difference" is simply a propaganda spin. There are far more differences than students are allowed to hear about in their classes. I have indicated many (there are many more). They should be able to objectively view all the evidence for and against and then decide for themselves (its called using critical thinking and encourages students HOW to think as opposed ti WHAT to think).

There is data and then there is the hypothesis based explanation added to the data (Ernst Mayr calls it "a historical narrative"). Students must learn (be taught) to distinguish between the two. Opinions in the subjunctive mood do not equal true beyond a reasonable doubt. Pick all those out and look at what is left.

 

[pshun2404]

Here is a great example though slightly off topic (if you will beg my pardon)

Bats, like turtles, are a great example of the “suddenly appearing fully formed” organism. It is agreed by most that bats arose somewhere about 80 to 100 mya. This means they were here at the same time as dinosaurs. They were present for the extinction event of 65 mya, and yet remained. From the earliest actual fossil for bats (56 mya) we can see with our own eyes that they have survived relatively unchanged, to this very day. Now that is not to say there are not many species for which intermediaries can be inferred from the data we do have.

But because there is zero evidence to show any transmutational evolvement for bats, a historical narrative has been contrived to make their fully formed presence fit the story we are taught.

The story tells us “we believe that” (the subjunctive bordering on Sci Fi) they began as some small aboreal creature which over thousands of generations jumping from tree to tree to get the insect food source, eventually developed gliding membranes similar to colugos, which eventually removed the need for fully functional front legs and these developed into wings. (how pseudo-Lamarkian is that)

This is ridiculous reasoning for such smart people, and I believe a kind of desperation. Why can’t students just look at the actual data and not have to be impressed with the Sci Fi or have their brains imprinted (like ours have been for generations) with artistically contrived images and convenient man made composites and filled in sometimes altered reconstructions? Why CAN'T we allow all the data (for and against) shape the theory, not the other way around?