Did humans descend from other primates?

[McCulloch]

Man did not descend from the primates.

Did humans descend from other primates?
Are humans primates or should there be special biological taxonomy for humanity?
Please cite evidence.

[otseng]

Category number 1 (Hierarchical Taxonomic Classification) is a good example of a pattern that can, of course, be explained by special creation. Linnaeus did just that. But Darwin a century later explained the same set of ordered relationships between organisms as being the result of divergent evolution and shared ancestry. More important, though, is the fact that organisms created de novo need not show varying degrees of similarity to one another. Each creature could be constructed completely differently from every other creature and made from very different materials. Humans need not look like apes, but we do. We show varying degrees of similarity to them and we are made of the same stuff. We could have been created this way but we must look like this if, indeed, we have evolved and diverged from a relatively recent common ancestor.

The article doesnt say taxonomy is necessarily the evidence, rather the fact that the similarities which taxonomy was based upon reveals to us patterns which can be explained by evolution. It is a way of answering "Why do this organisms look so much alike".

And also it states, "Category number 1 (Hierarchical Taxonomic Classification) is a good example of a pattern that can, of course, be explained by special creation".

So yes, they can be analogous or homologous, but its quite easy to separate the traits.

Can you give me an objective method to which something can be determined to be analogous or homologous? I have heard of no such method. Instead, it's a subjective call.

How do we decide if a character is homologous or analogous?

First we hypothesize them to be so. Then we look at the preponderance of other characters to test our hypothesis. Cladistics gives us a framework in which to do this. Cladistics was basically invented by Willi Hennig who was a specialist in flies. Here is a link to a site that describes in detail and in a different way how we do cladistics: http://www.ucmp.berkeley.edu/clad/clad1.html

In cladistics we assume that we wish to focus on genealogical relationships and that our classifications of taxa should depend on our analysis of these genealogical relationships. Of prime importance is the historical sequence in which the taxa descended from a common ancestor. Hence, our cladistic hypotheses are based on our estimate of the historical sequence of the acquisition of novel characters.

http://rainbow.ldeo.columbia.edu/courses/v1001/5.html

It would seem to me he stuck to the morphological classification and creation had nothing to do with it.

Here is what Carl Linnaeus wrote:

As he wrote in the preface to a late edition of Systema Naturae: Creationis telluris est gloria Dei ex opere Naturae per Hominem solum -- The Earth's creation is the glory of God, as seen from the works of Nature by Man alone. The study of nature would reveal the Divine Order of God's creation, and it was the naturalist's task to construct a "natural classification" that would reveal this Order in the universe.

http://www.ucmp.berkeley.edu/history/linnaeus.html

Even then, this is almost 300 year old science. Why would we try to use the views of a 300 year old scientist on creation today?

Why is it used as the first evidence in Humans As a Case Study for the Evidence of Evolution?

[Goat]

Category number 1 (Hierarchical Taxonomic Classification) is a good example of a pattern that can, of course, be explained by special creation. Linnaeus did just that. But Darwin a century later explained the same set of ordered relationships between organisms as being the result of divergent evolution and shared ancestry. More important, though, is the fact that organisms created de novo need not show varying degrees of similarity to one another. Each creature could be constructed completely differently from every other creature and made from very different materials. Humans need not look like apes, but we do. We show varying degrees of similarity to them and we are made of the same stuff. We could have been created this way but we must look like this if, indeed, we have evolved and diverged from a relatively recent common ancestor.

The article doesnt say taxonomy is necessarily the evidence, rather the fact that the similarities which taxonomy was based upon reveals to us patterns which can be explained by evolution. It is a way of answering "Why do this organisms look so much alike".

And also it states, "Category number 1 (Hierarchical Taxonomic Classification) is a good example of a pattern that can, of course, be explained by special creation".

Exactly how?? What can NOT be explained by 'special creation' ^TM .
How do you distinguish Special Creation from nature? Give the steps. So far, i see claims, but nothing to distinguish 'God did it' from natural explinations.

What is the actual evidence FOR creation? I want to see something more that "Oh, special creation can explain that too'.

Why does all evidence for this 'Special Creation' look exactly what you would expect if evolution was true?

[otseng]

As much as it is intellectually stimulating to think about your theories of Creationism, Why should I ignore the vast majority of fundamental scientists claiming your ideas are in error? We can't all be experts in biology, but why shouldn't I go along with the vast majority of scientists in the field, and agree with them as opposed to your ideas?

No, you shouldn't believe anything just because I say it. What it should be based on is the evidence presented. And if human evolution is indeed a fact, it should be quite simply to prove, without simply relying on the vast majority of scientists in the field agreeing with it.

[otseng]

What is the actual evidence FOR creation? I want to see something more that "Oh, special creation can explain that too'.

Why does all evidence for this 'Special Creation' look exactly what you would expect if evolution was true?

As stated repeatedly, I'm still waiting on the list of the tenets of human evolutionary theory, a list of predictions, and a list of ways to falsify it. When these lists are presented, I'll produce mine and the evidence to support my claims.

And I don't care who produces these lists. Anyone participating can present them. If, however, it is acknowledged that such lists cannot be produced, I'll go ahead and produce my lists and the evidence.

[Grumpy]

otseng

I'm still waiting on the list of the tenets of human evolutionary theory, a list of predictions, and a list of ways to falsify it.

Tenets? Evolution is not a philosophy, but Creationism is. Evolution is based on the evidence we see, Creationism is based on a book you read and the ideas it contains

Theory=Humans evolved from other, more primitive primates.

Predictions=brain size smaller, height shorter, weight less, less well developed walking(as opposed to grasping)feet, shorter lifespans, fewer and cruder tools as you go backward in time.

How to falsify these predictions=show how primitive hominids do not have these features, but are fully formed modern humans(as created 6000 years ago)in every case, even as we look further back in time. Oh, and show how our methods of dating are in error and how you explain them better.

If a god is powerful enough to create the Universe, you would think he could produce finished products that are as good as the materials allow, needing no improvement to fit the purposes of man, his ultimate creation. Yet modern man(Homo Sapiens Sapiens), in his relatively short time on Earth(20 thousand years at most), has used the forces of evolution(reproduction with modification, coupled with man's selection of desired traits)to create species that did not exist before. Some, like milk cows, cannot even survive a week without man's intervention. So, why would natural selection not be able to make those same degrees of changes to primates over millions of years? The only difference is the criteria of selection( survival or whatever man wants)and the method(death or man not allowing breeding). I think the principle is established beyond refutation.

Of course, we know that is exactly what happened, the evidence is pretty conclusive that evolution has occurred throughout the history of life on Earth(some 3.5 billion years), that all species descended from other, less well developed species and that every known creature, plant or bacteria are all related to the first chemical reaction we call life because we all speak exactly the same genetic language through DNA. A gene that produces spider silk does so in spiders or in goats, we are the same substances, obeying the same chemical rules.

Grumpy

[GrumpyMrGruff]

Which leads me to wonder, is there data showing roughly what percentage of mutations result in detrimental, neutral, and beneficial results?

Sorry, when you say mutations do you mean ERV insertions or any mutations? In the former case, I don't know of any papers trying to quantify the ratio of outcomes. In the latter case, there are many papers about the outcomes of single-nucleotide mutations in genes (whether silent (neutral) or not, and whether non-silent mutants are detrimental (many) or beneficial (a few)).

And another question, how do geneticists decide if something is an ERV?

During the part of their life cycles when retroviruses insert themselves into host genomes, they look like this.


Figure 1: Schematic of retroviral genome arrangement

Depending on the class of retrovirus, the arrangement of those genes varies and some classes have additional genes. That's the basic retroviral genome structure, though.

To find ERVs, researchers look at genomic sequence data for retroviral genes. Possible hits may look like these (many others are possible, but you get the idea):


Figure 2: Some possible ERV structures

The first case is the equivalent of a "completely intact fossil." All of the genes found in live retroviruses are present (though inactive) and in an order corresponding to a living class of retrovirus.

The second case gives another example of a "completely intact fossil," albeit a partially active one. The LTR still promotes expression of the GAG gene (it could easily be another viral gene), though without the full suite of retroviral genes this ERV is not pathogenic (in most cases). Sometimes expression of partially active ERVs can lead to autoimmune response[1]. Conversely, these genes (though initially neutral) may be co-opted by natural selection to serve host-beneficial functions.[2]

The remaining classes are "partial fossils." These partially deleted fragments may or may not have regulatory activity or gene expression, but they match the general arrangements of other retroviruses.

It seems peculiar that if an ERV insertion would be a remote event, that 8% of our entire genome would consist of leftover virus injections.

I checked the paper where this number originates.[3] This percentage includes the retrotransposons I mentioned previously - partially active ERVs (they can keep copying themselves in the genome but they can't make active viruses). Including this ongoing replication process can easily inflate the number or reported ERVs beyond those that are strictly due to viral insertions.


Figure 3: Schematic of retrotransposon structure
Look familiar? The POL gene (under the control of the LTR) allows the retrotransposon to copy itself. Without working copies of the capsid proteins (GAG) or envelope proteins (ENV), it cannot make new virus particles.

It seems to me there would be three possibilities of viral injections - pathogenic, neutral, functional. If it was pathogenic, it would cause the destruction of the cell, so the only thing left would be the other two.

Granted, but there's nothing to stop a neutral ERV from gaining a beneficial function. Regardless of whether such a beneficial mutation is passed to subsequent species, creationists shouldn't take issue with the initial neutral-to-beneficial mutation - it would be an example of "microevolution" within a species.

Also, the prediction that I mentioned before is that we will continue to find functions for ERV and that they will not all just be considered "defective" and "containing nonsense mutations". However, if they are all indeed found to be completely functionless, it would make more sense that it is an inactive remnant from an ancestor.

Let's look at the nitty-gritty of known ERV host-beneficial functions. The two main mechanisms in the literature are (1) regulation of host genes and (2) host use jury-rigged viral proteins (mentioned above).

First, consider how gene expression is regulated. Promoters are sequences directly upstream of genes. They recruit proteins to the DNA which transcribe RNA (in turn the template for proteins). The rate of transcription is further regulated by enhancers. The mechanisms of enhancers are poorly understood. They can be far from the promoter in the genome and still affect gene activity "at a distance."


Figure 4: Simplified schematic of gene regulation

How can ERVs affect gene regulation? The LTR sequence contains both an enhancer and a promoter. The LTR upstream of the viral proteins is the promoter for viral proteins. The downstream LTR is an artifact of the insertion process not used to promote viral proteins. However, it can effect host proteins:


Figure 5: Mechanisms of ERV gene regulation

In the first case, the ERV inserted between the host gene's normal promoter and the gene itself. The ERV's downstream LTR assumes control of the host gene. The remaining cases show how LTRs' enhancers may act "at a distance" to modulate host gene levels.

Whether these alterations are beneficial/neutral/deleterious cannot be predicted in advance. It depends if the new level of gene expression improves the host's reproductive fitness.

Note from the figure that even when ERVs are implicated in a gene regulatory function, they still have many inactivating mutations and defective viral genes. Why, when the LTR is the only structure needed for the host-beneficial function, did the designer include other inactivated viral genes?

Finally, how many ERVs actually regulate human gene expression? Enhancer function is difficult to quantify because enhancers needn't be near the genes they control. What about promoters? Recalling that there are many thousands of ERVs in the genome (including retrotransposons, which have active LTRs), this study evaluated 50,000+ ERV LTRs found less than 100 human genes under the control of ERV promoters.[4] Far less than 1% of known ERVs show this function - didn't the creationist position hinge on finding many, many functional ERVs?

Now consider the the second mechanism: Evolutionary conscription of viral proteins for host purposes. One of the best studied (of the few known) examples is the protein syncytin.[2] This protein shows high sequence similarity for the ENV protein. Like viral envelope proteins, it also functions in the cell membrane. Whereas viral ENV acts during infection to bind virus particles to host cells, syncytin modifies this function to fuse cell membranes in a syncytium.[5]Thus far you might attribute this similarity to analogous rather than homologous sequence. But if it is merely analogous, how how the surrounding genome structure looks like this:


Figure 6: Syncytium and surrounding sequence, adapted from [5]

Why do we observe inactive viral genes that are not required for the function of syncytin? Why does a designer include these functionless components when the ENV/syncytin is the only part that's required?

Again, why is it either-or? Why do they all need to be completely functionless?

It doesn't. My point is that if all ERV are found to be defective, then the most reasonable explanation is a common ancestor and not a common designer. If more functions are found, it becomes less reasonable. If a large majority of ERV are to be found with function, then it would be more reasonable to accept that it was designed.

I've made the case that, to the extent ERV gene regulatory function can be empirically evaluated, a very small portion of ERVs demonstrate this function. (You can hold out hope for enhancer functions.)

Even when this function is found, the creationist position must explain the seemingly less-than-frugal actions of their proposed creator.


Figure 7a: Would you litter your designs with unexploded landmines? A more intelligent plan for gene expression

Since LTRs are all that is required for gene regulation, why do we often see inactivated viral genes along side them (Figure 5)? These genes may be mutationally reactivated to cause diseases like cancer or MS. Why don't we observe patterns like those in Figure 7a (i.e., normal promoter or enhancer motifs without viral junk)?

Likewise, how do creationists account for the sequence around genes like syncytin?


Figure 7b: Why doesn't syncytin look like this?

The top image is a schematic of syncytin's genomic locus. The lower two alternatives present more intelligent "designs" without the potentially pathogenic viral junk.

This is the crux of the matter:

When people point out that the distribution of ERVs across species is evidence of shared ancestry, creationists attempt to circumvent this claim by suggesting that putative ERVs are not viral in origin but are specially designed. To bolster this claim, they suggest that function implies design (even though functional ERVs are completely consistent with evolutionary theory). Sure, there are ERVs with host functions. Not most ERVs, but some. However, creationists must present post-hoc explanations for the inclusion of non-functional viral components in host-functional ERVs. The most parsimonious explanation for these viral relics is retroviral insertion and subsequent natural selection. And if retroviral insertion is truly the cause of ERVs (functional or not), then the incredible odds against random insertion of the same viral strain at the same genomic locus across species provides incredibly strong evidence for shared ancestry. (The inescapable fact creationists were trying to avoid by invoking design of ERVs.)

This line of reasoning might hold in genes and regulatory elements controlling morphology (e.g., homeobox genes, bone morphogenetic proteins, hedgehog genes, etc., and their promoters), but it cannot logically be extended from morphological features to all genetic sequences in an organism.

Yes, I agree that it cannot be extended to all genetic sequences.

How does the creationist position account for the nested hierarchy of non-morphological genetic sequences? (Especially when this hierarchy is present even in silent mutations which CANNOT cause functional differences in different species' genes.)

Another question. Is it possible to compare an ERV and a virus genome and show that an ERV was derived from an actual virus? Can it be determined what actually mutated?

We can't find the exact virus that gave rise to an particular ERV. However, we wouldn't expect to. Retroviruses have RNA genomes and RNA is much more prone to mutations than DNA (because the RNA-to-DNA activity of reverse transcriptase is error-prone). By comparison, we can't find living copies of the 1918 influenza strain (an RNA virus) in the wild today and it is less than a hundred years old. This is the same reason HIV is so hard to treat; by the time it's diagnosed, there are so many mutant variants in the body that a fraction of them are almost guaranteed to be resistant to available drugs. Ironically, some ERVs in our DNA genomes may be closer to their progenitors than any extant retroviruses.

While we can't find the exact viral strain, we can compare the arrangement of endogenous viral genes with those in current retroviruses. I mentioned above that different classes of extant retroviruses have different arrangements of viral genes in their genomes. We can find these same arrangements of inactivated viral genes in ERVs, indicating which families of retroviruses they came from. There are also classes of ERVs for which we can find no surviving retroviral examples. Even through these viral remnants may not have any function in the genome, their viral functions can be recovered. Researchers have resurrected an ancient class of extinct ERVs by repairing the inactivating mutations.[6]

[sickles]

Did humans descend from other primates?

No.

I'll give my arguments in a later post.

Are humans primates or should there be special biological taxonomy for humanity?

I do not object to Linnaean taxonomy when its use is limited to its original intent. It was simply classification based on morphological features. However, nowadays, it has been hijacked to imply lineage.

Rather than having a special taxonomy for humans, the Linnaean taxonomy should be used only to describe physical features and not have any implications of lineage. If this is accepted, then I have no problem classifying humans as primates.

Research by Mary-Claire King in 1973 found 99% identical DNA between human beings and chimpanzees,[4] although research since has modified that finding to about 94%[5] commonality, with some of the difference occurring in non-coding DNA.

Similarities do not necessarily mean lineage. It could also mean they were designed is a similar fashion. HP and Gateway computers share many similarities, but they did not derive from the other.

Also, the percentage of identical DNA does not equate to the same percentage similarity in form, function, and behavior. Further, as you cited, the oft quoted 99% similarity between man and chimps is not accurate, and the more recent research has placed it at 94%.

Also, as far as I know, no evolutionist claims that there is a direct lineage from a chimp to a human. So, even if there are similarities, a chimpanzee would not show how humans evolved from primates.

Edit:
Corrected from "there is no direct lineage" to "there is a direct lineage"

what about the 1%-4% neanderthal DNA that all non africans possess? how do you explain this, if not through lineage?

[otseng]

Predictions=brain size smaller, height shorter, weight less, less well developed walking(as opposed to grasping)feet, shorter lifespans, fewer and cruder tools as you go backward in time.

The average height and size of Homo heidelbergensis is larger than humans. Cranal capacity is also quite large.

"Homo heidelbergensis had a larger brain when compared to other hominid species, and a body type which appears to be very similar to that of modern humans, although Homo heidelbergensis was somewhat taller."
http://www.wisegeek.com/what-was-homo-h ... gensis.htm

"The species was tall, 1.8 m (6 ft) on average, and more muscular than modern humans."
http://en.wikipedia.org/wiki/Homo_heidelbergensis

"H. heidelbergensis had a larger brain-case, up to 1400 cc, more than the 1350 cc average of modern humans."
http://news.softpedia.com/news/Top-10-E ... 2131.shtml

"He resembled a modern human but was more robust and slightly taller, averaging about 6 feet in height for adult males."
http://wiki.cotch.net/index.php/Homo#Ho ... lbergensis

How to falsify these predictions=show how primitive hominids do not have these features, but are fully formed modern humans(as created 6000 years ago)in every case, even as we look further back in time.

As mentioned in the links above, Homo heidelbergensis is similar to humans, but just larger.

[otseng]

Human Creation Model:
- God created the first man and woman (tens of thousands of years ago).
- God created the first humans distinct from the animals.
- All humans arose from the first couple.
- A global flood occurred. Noah and his sons and all their wives were the only humans (total of 8) to survive. They repopulated the Earth near the Middle East.

Predictions:
- All humanity traces lineage to one man and one woman.
- There is no gradual transition from animals (specifically primates) to humans.
- Humanity traces origins to around the Middle East area.
- Origin of man traces to tens of thousands of years ago.
- Greater genetic diversity of females than males during the Flood. Males were direct descendants of Noah. Their wives were not direct descendants of Noah's wife.
- Human culture should appear quickly in history.

Falsified by:
- A gradual transition is found from animals to humans in the fossil record.
- Genetic changes from one species to another and leading to humans are identified.

[nygreenguy]

Human Creation Model:
- God created the first man and woman (tens of thousands of years ago).
- God created the first humans distinct from the animals.
- All humans arose from the first couple.
- A global flood occurred. Noah and his sons and all their wives were the only humans (total of 8) to survive. They repopulated the Earth near the Middle East.

This is messed up in so many ways. You propose an untestable causal agent. That right there kicks it out of science.

Predictions:
- All humanity traces lineage to one man and one woman.

How does this seperate itself from evolution?
- There is no gradual transition from animals (specifically primates) to humans.[/quote] We dont see this

- Humanity traces origins to around the Middle East area.

How does this differ from evolution?

- Origin of man traces to tens of thousands of years ago.

Evidence proves otherwise

- Greater genetic diversity of females than males during the Flood. Males were direct descendants of Noah. Their wives were not direct descendants of Noah's wife.

This violates almost every ecological principal known to man.

- Human culture should appear quickly in history.

This doesnt prove anything. The development of writing can lead to this.

Most of your predictions can be explained by something else, making your predictions useless to proving your hypothesis.

- A gradual transition is found from animals to humans in the fossil record.
- Genetic changes from one species to another and leading to humans are identified.

done and done.