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Humans aren't apes... but biologically how?

hecd2

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Aside from the skewed interpretation of data included right in the OP it answers the question "Biologically, how aren't humans apes?" They are as uniquely different from apes as apes are from monkeys...
Have you got a reference for that assertion, or is it just your belief?
 
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hecd2

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Indeed it is quite common for individual species to be able to hybridise and even produce viable offspring (the biological definition of species is that they do not interbreed in the wild). That is the case with many members of the Felidae. But it is also a fact that any member of the Felidae cannot prouce viable and fertile offspring with any other member.

And it is the case with the Old World monkeys, and the gibbons, both families. As far as the old world monkeys, they are a very diverse group. There are extensibve reports of hybridisation within genera but not so many between genera. And gibbons form four genera with different chromsome counts and there are no reports of fertile hybrids between genera. So in just these two families, even if we accept that some hybridisation can occur with viable fertile offspring, then you have a lot more than two "kinds".

Your case is shot whichever way you turn. If you equate "kinds" with "can interbreed successfully", then you have a lot more than seven kinds in the Haplorrhini, and you have to explain how the same gene came to be mutated in the same way in all these "kinds". On the other hand, if you equate "kinds" with families, then you're skewered, because humans and chimps are in the same family.

And in any case, it's astronomically unlikely that even in a case of two taxa, say humans and chimps, that the same gene will be independently broken in the same way with an identical set of accumulated mutations.

ETA: it's also clear that you don't have a good definition of "kinds".
 
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hecd2

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I understand the distinction, but Xianghua's premises are logically inconsistent. He is proposing the example of a car as something that is self-evidently designed and then asserting that it can reproduce. The set of cars and the set of things that can reproduce do not intersect, so the object he is proposing has logically contradictory properties. It violates the basic logical principle of the Law of Non-contradiction. This is illustrated well by people who have used the examples of tringles and squares in this thread to illustrate his fallacy. No argument built on his premises can succeed (or even make sense).

It is only evidence for common descent in classes of things that have descent. It cannot be evidence for common descent in cars, because cars do not reproduce.

Cars don't have parents.
 
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hecd2

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And yet when comparing humans and chimpanzees across a wide range of anatomical, biochemical and genetic traits, the consensus view of phylogeneticists is that chimps and humans are more closely related than chimps and gorillas, or chimps and orangutans. That's the way the data pans out. Nobody claims that chimps are identical to humans, the claim is that humans and chimps are closer relatives than chimps and other great ape genera. To succeed in your argument, you'd have demonstrate across a huge range of criteria, including biochemistry and genetics, and not just the ones that differ, that humans are more different from chimps than chimps are from the other great apes. (For the avoidance of doubt, when I use the word chimp in this post, I mean chimpanzee and bonobo).
 
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Warden_of_the_Storm

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The pongidae classification was dissolved, and no longer used, by DARWINIANS (who at the time were all racists) who were trying to make man into ape or ape into man.

Okay, just so you know: in my eyes, everything you say is now completely useless because you made that claim.
 
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Warden_of_the_Storm

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I think that the reason you're not 'the most popular guy' is because you approach everything with a serious air of condescension and you also reek heavily of being an arm-chair scientist with the regard to you saying that scientists aren't looking at the facts 'objectively'.
 
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hecd2

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There is more than one way to compare genome similarity, so you need to make sure you are not comparing apples with frogs. The key question is whether the difference between human and chimp genomes is greater or less than the difference between chimp and gorilla genomes, using the same measure. Do you know the answer to that? And do you know how many of the base pairs in the genome actually have phenotypic consequences? And did you know that even in functional parts of the genonme, synonymous differences have no phenotypic consequences? And did you know that that in the vast tracts of non-functional sequences that not under selection, nucleotide differences make no phenotypic differences and are not conserved? The fact that you want to compare the entire genomes tells me that you don't understand these details.

In your opinion it's the very best and most complete study; and yet it pre-dates the first publication of the draft chimpanzee genome by three years. Since then the chimpanzee and human genome projects have had 13 years to increase the coverage and determine detailed polymorphic maps for each species, and refine the analysis. Buddy, you need to catch up.

The 2005 study, which is here, compared 2.4 billion bases and puts the nucleotide divergence at 1.23% with 14% to 22% of that being expained by within-species polymorphism.
 
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hecd2

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Read the studies!
I think you should take some of your own medicine. Since you don't seem to have read any of the studies that are more recent than the one you keep going on about, I would say your views are completely out-of-date.
It was a figure derived from studying selected portions hence not nearly a representation of the complete package.
And yet the more recent draft chimp genome study from 2005, had coverage of 2.4billion bases and found 1.23% nucleotide difference.
Add to that that most scientists disagree and say more like 4 to 5% (that from including other factors) the picture immediately begins to change.
Most scientists say 4% - 5%? Who are these "most scientists" , pray tell?

Did you know that there was a three-way study of human, bonobo and chimp published in Nature (The bonobo genome compared with the chimpanzee and human genomes) with much greater coverage genomes than the 2005 study and it says: "On average, the two alleles in single-copy, autosomal regions in the Ulindi (name of bonobo sequenced) genome are approximately 99.9% identical to each other, 99.6% identical to corresponding sequences in the chimpanzee genome and 98.7% identical to corresponding sequences in the human genome." The autosomes are all the chromosomes other than X and Y. You need to abandon this erroneous idea that the sequence similarity estimates are based on tiny samples.

The gap before Australopithecus has been filled since Mayr wrote by Sahelanthropus tchadensis, Orrorin tugenensis, Ardipithecus kaddaba and Ardipthecus ramidus. Ardipithecus is the earliest known bipedal ape. There really isn't a gap between Australopithecines and Homo, the latest Australopithecines overlap with the earliest Homo.

And from the Ruiz-Orera paper you reference:

"The advent of massively parallel RNA sequencing (RNA-Seq) has provided new clues to this question, with the discovery of an unexpectedly high number of transcripts that do not correspond to typical protein-coding genes, and which could serve as a substrate for this process. Here we have examined RNA-Seq data from 8 mammalian species in order to define a set of putative newly-born genes in human and chimpanzee and investigate what drives their expression. This is the largest-scale project to date that tries to address this scientific question. We have found thousands of transcripts that are human and/or chimpanzee-specific and which are likely to have originated de novo from previously non-transcribed regions of the genome. We have observed an enrichment in transcription factor binding sites in the promoter regions of these genes when compared to other species; this is consistent with the idea that the gain of new regulatory motifs results in de novo gene expression." To fully understand this, you need to understand the difference between transcription and translation and the effect of transcription factor binding. To paraphrase, the orphan genes appear to arise from previously non-transcribed portions of the genome.

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).
Except for the insight in the very paper you cite.
 
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hecd2

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No we are not placed in that box because the data doesn't support it. On the one hand you say there 4 - 5% difference between human and chimp and now you say there 1% difference between human and mouse. Needless to say you are misunderstanding something, misquoting something, or being deliberately misleading. (A reference to the 1% difference bewteen human and mouse would be a good thing to provide).

The data, that we are genetically closer to chimps, than chimps are to gorillas or orangutans is the data that shapes the hypothesis and the conclusion.
 
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sfs

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The 2005 study, which is here, compared 2.4 billion bases and puts the nucleotide divergence at 1.23% with 14% to 22% of that being expained by within-species polymorphism.
I pointed this fact out to him two years ago.
 
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DogmaHunter

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Humans are simply CATEGORIZED as Apes (to fit the hypothesis).

Not "to fit the hypothesis". Because of the evidence.

Biologically "what is an ape"? Not "categorically", biologically...

From Ape - Biology-Online Dictionary

Ape

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Definition

noun, plural: apes

Any of the tailless anthropoid primates of Hominoidea, which includes the great apes and the lesser apes

Supplement
The apes are a group of anthropoid primates belonging to Hominoidea. The members of Hominoidea are called hominoids. They may be grouped into two: (1) the great apes and (2) the lesser apes. The great apes or the hominids include Pongo, Gorilla, Pan, and Homo genera. They belong to the family Hominidae. The lesser apes of the family Hylobatidae is comprised by four genera of gibbons. The lesser apes differ from the great apes in having a smaller body frame and long arms they use to swing from branch to branch. The lesser apes also show low sexual dimorphisms.

The apes, together with the Old World monkeys, form the catarrhine clade. The apes are characterized by having a rather flexible shoulder joint, broad chest, long arms, and the absence of tail. Most of them are agile tree climbers and feed on fruits, nuts, seeds, leaves, etc.

Scientific classification:

  • Kingdom: Animalia
  • Phylum: Chordata
  • Class: Mammalia
  • Order: Primates
  • Suborder: Haplorhini
  • Parvorder: Catarrhini
  • Superfamily: Hominoidea [Gray, 1825
 
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pshun2404

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Okay. Now I would like you to please think about this with your truest honesty and objectivity. Here we have a real section of the compared genomes after being fed through one of the Algorithms intelligently designed to find areas of similarity. I am sure you are aware of the GIGO principle.

The programmers (already taught and convinced of the idea that humans ARE apes), designed a program that would ignore the obvious dissimilarity and focus on, in fact select, those areas where the sequence appears to be the same. However it is an unintentional deception and I will show you.

The top line represents humans and the bottom apes. When the algorithms are applied, we can see that in some places they do not match and in others unnatural spaces are created. The spaces do not exist in reality (the actual data). Aside from the more obvious G A difference, after the following AGTC section if we take away all the intelligently contrived spaces the two genomes remain dissimilar for the remaining over 2 billion sequences of base pairs.

Hence in reality, the two genomes are actually almost totally different if we just compare the two as they naturally occur making these two different kinds of creatures. As for containing similar sequences so what. We can find many of these in other creatures as well, and even in some fruits.

In truth we have:

Humans: AGTCGTACCAGTCGTACC

Apes: AGTCATACCAGTCTACCG

Once again I will remind you that we KNOW that even a change or mutation of a few base pairs can cause incredible changes in form or function and mostly (if occurring within the same creature) can and often does cause horrific medical deformities and conditions (like from particular mental deficiencies, to cystic fibrosis or sickle cell, and so on).

Now in truth, at least in chimps, we see many “shared genes.” But what you are not taught is revealed in some of the studies I already referenced.

a) Many of these genes contain very different sequences in the two creatures (some are larger and some are smaller).

b) Some pf those that are exact have a totally different function and purpose (same gene functions differently). In other words same genes different effects.

c) Many products (particular proteins coded for) are produced from entirely different genes in each creature. In other words same effect from different genes.
 
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hecd2

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Why do you keep quoting these outdated studies? Complete genome analyses have been available since 2005.
There you go again with the outdated studies. And yes indels can be anything from 1 to 100s or even 1000s of bases.

Who selected just these sections, their varying lengths, and why? How many of the same sections were compared from different humans and different chimps, or were they from just one of each?
Within species polymorphism is studied in depth in chimpanzees and up the wazoo in humans. The human polymorphism database is vast and growing. But I predict you are going to ignore this, like you have dishonestly ignored all the reports since 2002 and just come back with the same fallacy after a decent (or an indecent) interval. but we've been doing whole genome comparisons for 14 years. You do need to catch up. And stop ignoring the papers that falsify your position.
 
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hecd2

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I keep "using that phrase" because unlike many young earth creationists (of whom I am not) who often think up ever newer criticisms, I actually apply critical thinking skills and do my homework.
Well it seems that you don't if you think the best and most complete human-chimp genome comparison dates from 2002.

It's not, because humans are genetically (and biochemically) closer to chimps than chimps are to gorillas or orangutans.
 
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pitabread

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As a recent joiner I didn't know this, and I'm surprised because he states it as though no-one has corrected him before.

A lot of creationists on this forum have a bad habit of doing just that. It seems to be creationism 101.
 
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hecd2

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It's a very short sequence consisting of 18 or 19 bases.


OK, here is what is wrong with your analysis

1) what are the actual species? The top line is clear. Are you claiming that the bottom line is the sequence in all non-human apes? You don't say so we don't know if there is a frameshift deletion in humans or a frameshift insertion in a species of ape.
2) Where is this sequence found? Is it within an exon, in an intron, or in repetitive or other non transcribed sequence?
3) Assuming we are in an exon, we don't know where the open reading frame starts so we don't know whether the substitution A to G is synonymous (TCG and TCA code for the same amino acid - serine).
4) we have no idea what protein this codes for (or whether it's part of an ORF at all), so we don't know whether the substitution has a phenotypic effect and if so, how significant it is.
5) If we are in an exon we don't see whether the indel causes a fatal frameshift so that the gene is broken. Are both of these sequences functional in both species?
6) I can't believe you are claiming that because of one indel the entire 2 billion bases following are dissimilar. That shows a lack of understanding of genes and start and stop codons and transcription and splicing and open reading frames that is so profound that I'd say it entirely disqualifies you from discussions of genomics. I have emboldened this because this is a huge mistake on your part.
7) The key point, which has been repeated several times, is not whether humans and chimps share similar sequences, but whether the overall similarity is greater than that bewteen chimps and gorillas, and chimps and orangutans.

It can but mostly it doesn't, because they might be occurring in non-transcribed areas, or because the substitution is synonymous, or because the change from one amino acid to another has little or no phenotypic effect. Every human is born with between 60 and 75 new mutations in their genome (about 4 in protein-coding genes). A vast majority of mutations are neutral or have minor effects. There are several hundred thousand SNPs known in humans and the human population is more than 6 billion more or less healthy individuals. [ETA: Actually there are several hundred million SNPs known in humans - I mis-spoke]

And yet we are genetically closer to chimps than chimps are to gorillas.
 
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Job 33:6

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As a recent joiner I didn't know this, and I'm surprised because he states it as though no-one has corrected him before.

Its interesting because, I came to these forums not that long ago (about 9 months ago). I entered discussions with people like pshun. But unfortunately, I gave them the benefit of the doubt and went down the rabbit hole of the bizarre young earth creationist mind. Only to find that they were gone long long before we ever even began our discussion. Their minds, lost at sea.
 
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hecd2

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You can see the exchange here.
I've just read the first few pages of that thread. It's not just that he makes the same refuted arguments in this thread that he made in that one, but the words are identical. It's an unthinking cut and paste as though that thread and the complete demolition of his ideas there had never happened. People like Kent Hovind do that over and over and over again. Same MO.
 
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