Chimps and humans: How similar are we really?

[pshun2404]

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?

 

[AirPo]

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?

Out of how many?

 

[[serious]]

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?

I can break it down for you a bit. From the abstract of the paper: " the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins."

Basically, the theory the paper presents is that random mutation can create a start codon thus making a transcribable, if useless, new protein. Some subset of those new proteins may end up with a selectable function and be refined into new genes proper.

The specific gene mentioned in the bit you quote is specified to be an antisense gene. That is, it was on the opposite side of some other gene and ended up becoming a gene in it's own right. That would be the origin of that one.

 

[PsychoSarah]

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?

Only 1307?

 

[pshun2404]

I can break it down for you a bit. From the abstract of the paper: " the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins."

Basically, the theory the paper presents is that random mutation can create a start codon thus making a transcribable, if useless, new protein. Some subset of those new proteins may end up with a selectable function and be refined into new genes proper.

The specific gene mentioned in the bit you quote is specified to be an antisense gene. That is, it was on the opposite side of some other gene and ended up becoming a gene in it's own right. That would be the origin of that one.

I can see how given billions of years the unique combinations of alleles and the rare mutations which remain (discounting the majority of detrimental ones) could bring about such differences...except I would suggest that there are a much larger number of differences than the media presentations would lead us to believe...they would like us to think we are variations of the same creature at some point, but the data does not necessarily demonstrate that to be true, only possible. The genetics IMO only show the reasons for our physically all being mammals and then primates within that classification.

Just because something precedes something else does not necessitate that the primary causes the secondary, nor that something preceding two things is related to producing either or both. It COULD BE possible and even MAY BE possible but we do not know, and thus should not rhetorically present these subjunctives as truth.

Take statistics for example (and I know you know this), what sample, how large, from where, etc., all effect what the statistic could or may imply. Also from a number of statistical tests on the same subject matter often the tester decides or chooses the results needed to support their pre-concluded view or must use a line of best guess (which in itself can be deceptive based on the other factors mentioned above...the sample size, the who, the what, the where, the when, etc.)

The orphan genes are much more objective than these other areas (like the less than 2% genomic claims) and this explanation is totally reasonable. This however still does not necessitate a common ancestor.

 

[pshun2404]

Only 1307?

So far....

 

[Loudmouth]

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.

Completely?

Even two random sequences will have the same base 25% of the time. Please show us a comparison of the orphan genes and any homologous sequence in the other genome.

From what I can read, there is a lot of homologous DNA for these orphan genes in other species. What appears to have happened is small mutations have resulted in the expression of already existing sequence. Even then, the vast majority of these orphan genes are less than 100 amino acids long which means they make up a tiny portion of the overall genome.

 

[Loudmouth]

I can see how given billions of years the unique combinations of alleles and the rare mutations which remain (discounting the majority of detrimental ones) could bring about such differences...except I would suggest that there are a much larger number of differences than the media presentations would lead us to believe...

Why?

In this example, you are pointing to less than 0.1% of the genome. If we are very generous, each gene is 1,000 base pairs or less. 1,300 genes is 1.3 million bases. The human euchromatic haploid genome is 3 billion bases. 1.3 million is just 0.004% of the genome. Even if every single base were different, it is just a 0.004% difference for these orphan genes, and that is being very generous since most are less than 100 amino acids (300 base pairs). The reported difference between the human and chimp genome is said to be 35 million substitutions and 5 million indels. Can you please tell me how your 1.3 million mutations puts those numbers in doubt?

Perhaps you should do the math before making grand pronouncements about the entire scientific community being wrong.

 

[Steve Petersen]

Chimps and humans still share about 95% of their genome.

 

[pshun2404]

Why?

In this example, you are pointing to less than 0.1% of the genome. If we are very generous, each gene is 1,000 base pairs or less. 1,300 genes is 1.3 million bases. The human euchromatic haploid genome is 3 billion bases. 1.3 million is just 0.004% of the genome. Even if every single base were different, it is just a 0.004% difference for these orphan genes, and that is being very generous since most are less than 100 amino acids (300 base pairs). The reported difference between the human and chimp genome is said to be 35 million substitutions and 5 million indels. Can you please tell me how your 1.3 million mutations puts those numbers in doubt?

Perhaps you should do the math before making grand pronouncements about the entire scientific community being wrong.

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.”


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! The actual difference is more like 5% (National Geographic claims 4% but close enough to show the smaller number to be enhanced) and most scientists agree.


In the limited sections of the genomes accessed, exploring the limited aspects of the genome that they used to derive these dwarfed figures, it is understood that the common person will not understand and most are simply persuaded by the appeal to authority fallacy,and by faith in statistics (see How to Lie with Statistics,by Darrell Huff…a must read for any statisticians).


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. Though this sounds huge, it is not….it is really quite miniscule. Nothing learned in this study should be generalized as an overall fact. In addition, in the Britten study (Britten, R.J. 2002. ‘Divergence between samples of chimpanzee and human DNA sequences is 5% counting indels.’ Proceedings National Academy Science 99:13633-13635) used only 779,000 base pairs. The study concludes 1.4% of the bases were “substitutions” (meaning completely different, and not actually once one thing that has been “substituted”), BUT they also found an additional number of indels (what can be “interpreted” as insertions or deletions when comparing one genome to another). As you pointed out, some were as small sections being only 1 to 4 nucleotides in length, but actually others were quite large (even as much as 1000 base pairs long). These additional indels should have been added into the alleged “percentile” similarity/difference conclusion.


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 (which again has never actually been done). But without going off into all that, when we take the Chimp vs. Human “differences”, as slight as even 5 % may sound, that difference is HUGE.


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).


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).


Why not just say we have found at least 120,000,000 differences? When stated like that (just the data)…if we count the number of possible functions and forms possibly effected, IMO it’s like the difference between arithmetic and calculus. The amount of information encoded in over 120 million base pairs is unfathomable. Plus we have barely scraped the surface of what this means. It is actually more information than a whole think tank of genius level scientists could ever contain in 10 lifetimes compared to a think tank with only the knowledge held by any general group of common persons in 10 lifetimes. See the difference? Vast, and incomprehensible, to say the least.


I guess what I would like people to see is how when we look at declared statistics of the very same genomic portrait from a different prospective area of approach, what a different picture we get.


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?

 

[Derek Meyer]

I'm not really too sure why you write this. The technology used is the same in determining how closely you are related to your parents and to your grand parents and to your brother or sister or to your son or to your cousin or to a chimp or to a gorilla or to a lion or to a fish or to a daffodil or to a bacteria.

It doesn't matter how you measure the relatedness by genetics, the tests always show that I'm more closely related to my father or mother or brother or sister than to your grand father or grand mother or cousin. It doesn't matter which version of any of the tests you use. And that I'm always more closely related to my biological family than to some Mr Smith living in Utah. And also that I'm more closely related to Mr Smith in Utah than to bonobo's. And also more closely related to bonobos than to gorillas. And also more closely related to gorillas than to lions. And more closely related to lions than to fish. And more closely related to fish than to daffodils. And more closely related to daffodils than to bacteria.

Word salads won't change that.

 

[Derek Meyer]

This one really was funny.

Secondly, some wouldn’t the 2nd law of genetics tell us...

Comedy central.

 

[pshun2404]

1. We are all living creatures (thus we have functional DNA and a set of basic genetic information relative to "living creature" verses rocks and minerals and free energies)
2. We are all physically Mammals (thus we have common DNA with all other Mammals and exhibit similarity...hair, genitalia, mammary glands, etc.)
3. We are all physically part of the man made category "Primate" (So we have common DNA with all other Primates and that gibes us similar characteristics)
4. We physically share anatomical and physiological traits with certain primates (So we have common DNA with all others in that sub-group to produce those qualities)

That does not mean they are our ancestors, just that we have similarity in our form design for our functionality as opposed to a rodent or an elephant....

 

[AirPo]

1. We are all living creatures (thus we have functional DNA and a set of basic genetic information relative to "living creature" verses rocks and minerals and free energies)
2. We are all physically Mammals (thus we have common DNA with all other Mammals and exhibit similarity...hair, genitalia, mammary glands, etc.)
3. We are all physically part of the man made category "Primate" (So we have common DNA with all other Primates and that gibes us similar characteristics)
4. We physically share anatomical and physiological traits with certain primates (So we have common DNA with all others in that sub-group to produce those qualities)

That does not mean they are our ancestors, just that we have similarity in our form design for our functionality as opposed to a rodent or an elephant....

We have similarity in our form design for our functionality with rodents and elephants.

 

[David4223]

MOD HAT ON

This thread has been moved from the Physical and Life Sciences forum to the Creation and Evolution forum as staff feels that it more closely fits in with that forum.

MOD HAT OFF​

 

[pshun2404]

Why? It speaks directly to "life science" theory and is not debating "creationism"...and thus it should be put back...please feel free to post it in both if you wish but do not remove it....

 

[pshun2404]

We have big brains (1100 cc to 1500 cc) they have small brains (300 cc to 600 cc)…

We are bi-pedal and they are knuckle walkers,

We have pronounced chins they have small receded chins,

We have a big toe in line with our other toes and they have opposable or separated big toes, ours for balance and walking, theirs for grasping and other forms of manipulation…

We have very different skeletal structures…

We have rounded craniums and a flatter face, they have a flatter cranium with a pronounced sagittal crest and protruding lower face (better for biting adversaries)…they have a distinctly protruding brow ridge (which varies to a small degree) and we have a far less protruding brow ridge (which varies to a small degree)

The difference in the orbital socket allows us to see laterally for more than any ape but definitely more than chimps (their skull hinders viewing freely to the sides). Our eye sockets are allegedly wider relative to our height than a chimps and in humans the outer margin is recessed much further back.

Chimp teeth demonstrate a need as a weapon and a show of dominance as well as for eating, where humans teeth are smaller, more regular, for eating (and sometimes part of attracting mates)

Our pelvis is properly designed for our distinctly bi-pedal gait, the chimps is longer and narrower for knuckle walking, Humans by nature are bi-pedal except for short bursts of walking on all fours, chimps are arboreal knuckle walkers with short bursts of standing or walking upright.

Our spines are long and straight for energy efficiency and support, the chimps is bent differently and positioned so their heads can jutt forward for walking on all fours,

We exhibit 3 main morphological types (Neanderthal Sapiens, Denisovan Sapiens, and Sapien sapiens) chimps do not demonstrate different morphological types,

Chimp-kind is only found in Africa, while human-kind is found everywhere in the world,

Chimp intelligence is dwarfed compared to even the lowest examples of human intelligence,


Humans live long compared to chimps,


Humans demonstrate things like uniqueness of culture, religion, philosophy, abstract thinking, art, intricate application of symbolic thought, and more, where chimps exhibit none of these things,

We have a covering of fine hairs and theirs are thick, course, fur.


The best of signing chimps only know objects wanted or not wanted, and learn specific phrases taught by conditioning in order to get food, petting, sex, and so on.

Human communication (language) utilizes vocabulary but also syntax. For chimps "give orange me," can mean something totally different than "give me orange" even among different signing chimps. We can condition them to sign “give orange me” to ask for an apple and “give me orange” to say they are tired now….they do not get confused or associate the difference…On the other hand, from a very young age, humans understand this. If your two or three year old asks for some orange and you gave them apple, they would protest or say “No! Orange not apple”…or at least exhibit confusion

We have an innate ability to create new meanings by combining and ordering words in diverse ways. Chimps studied, taught, and even conditioned for years, show no such capacity.

Human children demonstrate the ability (on their own) to vary syntax and express related ideas and concepts (sometimes vert abstract) while even the most mature chimps, trained from birth show no propensity of being able to produce this variance to either communicate with others or even to get their own way.

Cognition scientists have concluded after half a century of research that “chimps” are unable to infer the mental state of another, whether they are happy, sad, angry, interested in some goal, in love, jealous or otherwise, while even 1 and 2 year old humans can do this (see the Project Nim documentary). In addition, even trained “chimps” do not conversate with other individuals though as individuals they do demonstrate some basic emotions (anger, rage, happiness, grief, depression, etc.)

Just more to consider from a Homo Cognitarus

 

[Papias]

It ... is not debating "creationism".

what? you explicitly disagreed with evolution in posts #5 and #13, implicitly in all your other posts on this thread, and that's not including the fact that the title and OP of the thread are arguing that we are very different from chimps, our closest living relative according to evolution.

Seriously, pshun, you don't think your purpose on this thread to argue against evolution isn't completely clear? Why try to hide it? In fact, until this post, I didn't think you would want to hide that fact.

So much for the 8th (Protestant) or 9th (Catholic) commandment, I guess.

Papias

 

[pshun2404]

Seriously, pshun, you don't think your purpose on this thread to argue against evolution isn't completely clear? Why try to hide it? In fact, until this post, I didn't think you would want to hide that fact.

Why would you choose coming in so late to misrepresent me? I said I was "not debating creationism", and that is not the same thing as arguing against "evolutionism". In fact I am not arguing against evolution at all but rather against the "evolutionism" that sneaks through. My point is, make all the data available and then let the thinker decide for themselves.

I believe in evolution, I see it every day, and in so many ways, but that does not mean I accept every premise made by every evolutionist (again that's quite different)...I am not throwing out the baby with the bath water. The OP asks how similar are we? I am presenting data concerning our differences...all of which is true. We are also very similar in many ways, that not equaling one came from the other, nor that both came from a common ancestor. Those conclusions are inducted from having already accepted the hypothesis (which I also did for decades)...

I believe we need to accent our differences as much as our similarities...does such objectivity pose a problem?

 

[[serious]]

We have an innate ability to create new meanings by combining and ordering words in diverse ways. Chimps studied, taught, and even conditioned for years, show no such capacity.

Your post is long and I'm on my phone, so let me just pick out this part. Non human primates have been shown to combine words to form new concepts. https://en.m.wikipedia.org/wiki/Washoe_(chimpanzee)

I recall reading about novel combinations of words to form new words, but couldn't immediately find where