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.

[Scotracer]

What is it about humans that you believe is novel, as compared to the other primates?

I'll quote Juan Luis Arsuaga:

We are unique and alone now in the world. There is no other animal species that truly resembles our own. A physical and mental chasm separates us from all other living creatures. There is no other bipedal mammal. No other mammal controls and uses fire, writes books, travels in space, paints portraits, or prays. This is not a question of degree. It is all or nothing; there is no semi-pedal animal, none that makes only small fires, writes only short sentences, builds only rudimentary spaceships, draws just a little bit, or prays just occasionally.

The Neanderthal's Necklace: In Search of the First Thinkers

Well you're wrong on the 'semi-pedal' comment straight off the bat given that almost all primates can move biped-ally to some degree. Some are very good at it, and others not.

And again, many animals can draw/paint:

[youtube][/youtube]

The rest of the statements are a bit ridiculous given that if an animal can't use tools to any great extent, how are they to build spaceships? One follows the other.

You could create a list of features that are known only to itself, for just about any animal, really.

[McCulloch]

What is it about humans that you believe is novel, as compared to the other primates?

I'll quote Juan Luis Arsuaga:

We are unique and alone now in the world. There is no other animal species that truly resembles our own. A physical and mental chasm separates us from all other living creatures. There is no other bipedal mammal. No other mammal controls and uses fire, writes books, travels in space, paints portraits, or prays. This is not a question of degree. It is all or nothing; there is no semi-pedal animal, none that makes only small fires, writes only short sentences, builds only rudimentary spaceships, draws just a little bit, or prays just occasionally.

The Neanderthal's Necklace: In Search of the First Thinkers

OK, and I'll quote the linked review of the same book

The Neanderthals provide a surprising mirror for modern-day humanity. They belonged to our evolutionary group and lived like the Cro-Magnons, our ancestors, did — worshipping, socializing, and hunting. The struggle between Neanderthals and Cro-Magnons lasted thousands of years. The Cro-Magnons were not biologically fit for extreme cold weather, but their ingenuity allowed them to settle down, band together, and survive. In this tale of life, death, and the awakening of human awareness, Juan Luis Arsuaga, Spain's most celebrated paleoanthropologist, depicts the dramatic struggle between two clashing species, of which only one survives.

[font=Times New Roman]emphasis mine[/font]

I contend that the distinctiveness of the human species is a matter of degree not that there are any qualities that are unique to us. Even the author you cite agrees that the apparent uniqueness of humanity is not sufficient to exclude an evolutionary explanation.

There is no other bipedal mammal. There are no other primarily bipedal mammals but other mammals do have bipedal abilities and bipedalism is rather common for birds. But, it is in our thinking and communication that we stand out from the other species. Yet, even there, there is less difference between the mental abilities of a typical human and a typical chimpanzee than there is between a typical chimpanzee and most invertebrates.

[Grumpy]

otseng

there is no semi-pedal animal

Bonobos

draws just a little bit

elephants

writes only short sentences

Again, bonobos(but there are several other examples in chimps and orangutans


Examples of Kanzi's behavior


Paul Raffaele, at Savage-Rumbaugh's request, performed a Maori War Dance for the Bonobos. This dance includes thigh-slapping, chest-thumping, and hollering. Almost all the bonobos present interpreted this as an aggressive display, and reacted with loud screams, tooth-baring, and pounding the walls and floor. All but Kanzi, who remained perfectly calm; he then communicated with Savage-Rumbaugh using bonobo vocalizations; Savage-Rumbaugh understood these vocalizations, and said to Raffaele "he'd like you to do it again just for him, in a room out back, so the others won't get upset.� So a private performance in another room was successfully, peacefully and happily carried out.

Sue Savage-Rumbaugh has observed Kanzi in communication to his sister. In this experiment, Kanzi was kept in a separate room of the Great Ape Project and shown some yogurt. Kanzi started vocalizing the word "yogurt" in an unknown "language"; his sister, Panbanisha, who could not see the yogurt, then pointed to the lexigram for yogurt.

builds only rudimentary spaceships,

Neither did any man do so until the 1940s, this is a ridiculous statement. But a space ship is a tool...

"Kanzi's accomplishments also include tool use and tool crafting. Kanzi is an accomplished stone tool maker and can flake Oldowan style cutting knives. He learned this skill from Dr. Nick Toth, who is an anthropologist with the Stone Age Institute in Bloomington, Indiana. The stone knives Kanzi creates are very sharp and can cut animal hide and thick ropes."

In one demonstration shown on the television show Champions of the Wild, Kanzi was shown playing the arcade game Pac-Man and understanding how to beat it. "

http://en.wikipedia.org/wiki/Kanzi

none that makes only small fires

"In an outing in the Georgia woods, Kanzi touched the symbols for "marshmallows" and "fire." Susan Savage-Rumbaugh said in an interview that, "Given matches and marshmallows, Kanzi snapped twigs for a fire, lit them with the matches and toasted the marshmallows on a stick.""



Starts at minute 5:00, but the whole presentation is well worth the time.

or prays.

Not sure how Juan read the minds of any creature. And I'm not sure how praying is different in kind from cowering in fear of anything a creature does not understand.

Juan Luis Arsuaga does not seem to know what he is talking about, almost everything in the cite is wrong. Man's technology and our degree of intelligence are much greater than other apes, but it IS just a matter of degree, not a difference in kind.

Humans are apes, advanced beyond all other apes, but apes nonetheless.

Though I am glad to see you are finally admitting that the use of fire is an indication of being human. Man has used fire for over a million years and all creatures that use fire must be considered human. That's progress.

Grumpy

[GrumpyMrGruff]

Sorry about the delay. The real world intruded for a bit.

There's nothing wrong with extrapolation by itself. To reiterate my point, all I'm saying is that macroevolution is unobservable. I brought this up originally to counter the charge that a designer should be dismissed because it cannot be observed and revealing the inconsistency in the use of observability.

Trivially, any process that takes longer than a human lifetime (or the lifetime of human civilization) is unobservable. However, this is a different than saying that the mechanisms which underlie the process are unobservable.

We cannot observe a pair of galaxies colliding, passing through each other, and drifting apart. It takes too long. We can see galaxies in various stages of the process and we can apply observable mechanisms - mechanics – to parsimoniously connect the dots between observations.

We cannot observe stellar evolution from collapsing gas clouds to novas or dwarves. We can observe stars in all stages along this progression and we can apply observable mechanisms – nuclear physics and mechanics – to parsimoniously connect the dots between observations.

We cannot observe accumulations of genotypic/phenotypic variation which occur on super-human timescales. We can observe organisms with different morphologies over time (fossils) and a hierarchical pattern of genotypic similarity in living organisms. We can apply observable mechanisms – drift, mutation, and natural selection – to parsimoniously connect the dots between observations.

Note that I am proceeding under the assumption (which I haven't seen you dispute) that the most parsimonious (and therefore the best) method available for making inferences about the past (especially the prehistoric past) is to extrapolate backward from known, observed mechanisms.

Further, I am not suggesting that a designer be dismissed because it cannot be observed. I am suggesting that it is a less parsimonious explanation because such designers have not been observed. Invoking a designer requires more unconfirmed mechanisms than evolution and is less therefore parsimonious.

You have brought up this macro/micro distinction without illustrating any mechanistic difference between the two. Rather, you've drawn an arbitrary line within phenotypic characteristics. This seems like a category error, because the parsimony of an explanation does not require that anyone observe an unobservable (by definition) process. Rather, the parsimony of an explanation requires that the underlying mechanisms be observable. (And even if an explanation invokes mechanisms that are observable-but-not-yet-observed, it remains less parsimonious than consistent explanations which rely solely on observed mechanisms.)

You seem to be saying that I am employing a double standard invoking an unobservable mechanism, but you haven’t said what that mechanism is. You have only repeated the micro/macro distinction without explaining how they involve different mechanisms (or, equally important, why we expect a priori that the known mechanisms are insufficient). Conversely, you haven’t described any mechanisms of the proposed designer (and to my knowledge we haven’t observed the designer in action). How does the designer provide a more parsimonious explanation with fewer unknowns? (What known mechanisms are you extrapolating from?)

What I have shown is that from human experience in the domestication of animals, there is not much significant change in morphological features in animals to account for common descent.

You've provided an example spanning a few millennia. The timespan in question is millions of years. Why should we expect to see the same degree (quantitative) of genotypic change (and corresponding phenotypic change) on human timescales? Again, unless you will describe a difference of mechanism for macroevolution (i.e., why you have reason to suspect observed mechanisms are incapable of accounting for the diversity among species), you aren't making much of a case against the validity of the evolutionary extrapolation. The whole purpose of this exercise is to extrapolate beyond historic timescales (many times the scope of all recorded human experience, which goes back only some thousands of years).

Yes, I would agree that there is a subjective element to it. But even the term "species" is a bit subjective.

...

And since micro and macro is often differentiated at the species level by evolutionists, then the terms microevolution and macroevolution are also likewise subjective.

'Species' is a useful but arbitrary label. I maintain that there is no such thing as an ideal horse or ideal oak tree that exists independently of our minds - these are only labels we apply to biological replicator populations with similar genomes (and even the genetic contents of those populations change over time and generations). I'm all for the replacement of Linnaean taxonomy with something like Phylocode. But that's neither here nor there.

I'm not so sure there can be an objective evaluation [of macro- vs. microevolutionary traits] either. But, this would be a problem across the board.

I'm not sure what you mean by "across the board." I am maintaining that all differences in existing organisms stem from quantitative differences in genotype. I think that macro/micro is as arbitrary a categorical distinction as species. It's just as arbitrary, but not even as useful. At least in sexual organisms we can choose to define species by reproductive incompatibility (allowing us to keep track of gene flow). You've just stated that you don't have an objective method (however ad hoc) for telling micro/macro morphological traits apart.

We apply labels to the world to help us understand it, but those signifiers don't make the labeled objects intrinsically different. How does your micro/macro distinction help us understand anything?

I think the difference here is "similarity of function" and "morphological similarities". Two different morphological features could be used for a similar function. A hoof and a webbed foot can be used for walking, but are not similar morphologically.

This seems like a dead-end argument. To the extent that a bee wing and a penguin wing are both flat, digitless structures protruding from the dorsal side of the organism (i.e., wings), they’re morphologically similar. We could argue ‘similarity’ all day. Does your model provide any hard predictions about patterns of similarity in nature (either genetic or morphological)? Correspondingly, do these model predictions provide falsification criteria (patterns which falsify design if observed)?

[GrumpyMrGruff]

I can see no a priori reason to expect this pattern if the organisms were designed. Can you provide one? 'The designer could've done it that way' doesn't cut it. The designer could've done anything - you refuse to discuss the scope and limitations of its methods. What reasons do we have to think it should've done it that way?

I try not to use that as an explanation and I don't believe I've ever stated that here in this thread.

As I commented above, I think the best anyone can do is appeal to parsimony for model discrimination. We see a pattern in existing species and evolutionary biology provides a parsimonious and falsifiable explanation for that pattern based on observed mechanisms. Simply positing a designer does not make a designer more parsimonious (because it has not yet been observed if it’s even observable). Thus far you have been reluctant to discuss the designer’s tools (or we can call them mechanisms if you dislike ‘tools’). Trivially, if one posits a ‘designer that created all life such that it appears the way it appears,’ it is unfalsifiable (besides being tautological). This statement also has zero explanatory power. If somebody presented it to you, why would you even consider it?

In a previous post, you state that your skepticism regarding the evolutionary explanation for diversity of species stems from the inability to differentiate analogous and homologous structures. I’m not saying that you’ve argued the following specifically, but one could claim all animals (or all primates, or just humans) were specially created with the observed patterns of genetic and morphological similarity and no one could never falsify this statement.

Conversely, we have no reason to accept a model with zero explanatory power (and zero corresponding falsifiability). Sure, all organisms’ genes could be analogous creations of a designer (unfalsifiable). What reason do we have to think so? How parsimonious is this explanation in the absence of a known design mechanism for generating this pattern of analogous diversity?

The only way I can currently think of to falsify what I claim using molecular genetic evidence is what I stated earlier - "Genetic changes from one species to another and leading to humans are identified." For the purposes of this discussion, just the genetic steps from the common primate ancestor to humans would suffice to falsify the Human Creation Model. I would agree that modern genetics is not able to do this now. But, if it's ever done in the future, the model I proposed would be falsified.

Granting for the sake of argument that a viable evolutionary trajectory between chimps and humans could be found, it would not falsify claims of special creation for the reason given above. A dedicated creationist would have no reason to accept that, simply because a viable path exists, that path was ever actually traversed in the past. Certainly, such a finding would strengthen the evolutionary explanation (reinforcing the view that known mechanisms are sufficient to account for known biodiversity). Compare: If a creationist identified an Ice Age land-bridge between Asia and Australia, it wouldn’t obligate non-Christians to accept the additional claim that marsupials ever traversed it on their way from Noah’s Ark to Australia.

In order to be falsifiable, a model must do more than be consistent with previously collected data (that’s merely is a prerequisite for its consideration). It must make predictions about new data we may yet collect. This is why I am critical of your previously offered falsification criteria (evidence consistent with evolution rather than data inconsistent with any predictions of your model). Saying, for example, that mankind originated in the Mideast is at best a corollary to the premises of your model because it does not describe any new data we may collect (i.e., it’s not a prediction about the future). Describing (based on your model) what patterns of new data (archaeological, biological, anthropological) may yet be uncovered in the present day would constitute a prediction. And going further to describe patterns of new data which would be inconsistent with your model would constitute actual falsification criteria (unlike the two pieces of evolutionary evidence provided thus far as falsification criteria).

You claim that this only applies when multiple models are being compared:

I think this would apply if there was a third explanation on the table. If there are only two, then it is fair to compare and contrast the two.

I disagree. Both models need to be evaluated on their own merits to rule out the possibility that either of the models is actually unfalsifiable. I’ve shown how the mechanistic predictions of evolutionary theory provide a falsification criterion – patterns of genetic data incompatible with the theory. You have yet to show that your model is even capable of providing similar predictions and falsification criteria. (And if it can’t, why are we considering an unfalsifiable model?)

I was specifically addressing your point "You have been invoking a designer, but you have not specified any of the tools used by the designer (or the genetic artifacts left by those tools which we might observe today)." My point is not about the ability to detect design, but that knowledge of the tools used is not necessary.

Again, if you dislike ‘tools,’ how about mechanisms? I’m not talking about knowing the brand name of jackhammer used to carve Teddy’s nose, but rather the assortment of mechanisms available to fashion the sculpture. Let’s extend your Rushmore example. Mount Rushmore is suddenly transported to a mountain range on a distant planet. It is the metaphorical watch on Paley’s now-cosmic beach. An alien flies by. It has never seen humans (or human faces) – heck, it doesn’t even have eyes. How can it determine that Rushmore is artificial? Minimally, it needs to know the potential mechanisms used to construct it (contra the natural processes of the planet that may’ve formed it). If you disagree, would you please explain?

If [identification of all intermediate genomes between species] is even impossible in principle, then there'd be no way to unequivocally prove common descent through genetic evidence.

The scientific method never proves anything. You know that. And because we’re dealing with inferences about the past, the best we can do is construct parsimonious, falsifiable (but not falsified) descriptions about what happened pending acquisition of new data. Extrapolating backward from known evolutionary mechanisms provides such a description. I’ve already shown how it may be falsified.

If this is true (and if it's impossible to know the genome of extinct organisms), then it'd be impossible to construct a tree of life diagram based on genetics.

This is incorrect. Phylogeny constructs trees based on the nested hierarch of genetic similarity in compared sequences. Mutation, drift, and natural selection provide a parsimonious explanation for the recurrence of the same tree when sampling across different sequences (design provides no such a priori mechanistic explanation for this observation). Some phylogenetic software attempts to reconstruct ancestral sequences at internal nodes of trees, but this step is not required for the process. At any rate, the programs have no rigorous way to deal with insertions and deletions. Consequently, they have no way of reconstructing whole genomes because whole genomes contain many variable insertion/deletions as a result of things like retrotranposons and transposons (among other mechanisms).

What I've offered is the definitive proof and falsification of the theories. Can you offer then any other suggestions that would be the definitive proof and falsification of the theories?

I’d appreciate if you'd point out where you’ve offered “definitive proof,� because such proof is impossible within a scientific framework. Do you mean conclusive evidence? If so, where have you offered this? The best we can strive for is a predictive, therefore falsifiable (but-not-yet-falsified), parsimonious explanation that accounts for available data.

I’ve explained how known mechanisms can account for the genotypic (hence phenotypic) diversity of life and what new data can falsify this model. To date, the mechanisms of your creation model remain so vague that I have not seen any falsification criteria based on the model’s predictions. I’m still hoping you’ll provide some.

But, if you say that [reconstructing the extinct genomes from known genomes] would be impossible even in principle in the future, then I'll defer to you to provide methods to prove common descent.

You’re being a bit careless with ‘proof’ again. I can see this going back and forth for a long time. Do you agree that mechanistic, falsifiable, parsimonious explanations are the best we can do? If so, I think I’ve already made my case that evolution provides the most parsimonious explanation. I’m waiting for you to make yours.

One might see [competing hominid phylogenies] as evidence of human evolution. I see it as evidence of the intractability of being able to coming to a consensus of arranging hominid evolution to man.

My purpose with this figure was to show that you are demanding too high a resolution from necessarily incomplete data.

By comparison:
Your model predicts that all humans are related. If I exhume 100 ancient human skeletons and present them to you with the demand that you tell me their exact relationships (e.g., ‘This one is the 15th cousin of that one, twice removed’), you would tell me you don’t have enough data to go on. (Indeed, if you were provided the skeletons of every deceased human, this would constitute an insufficient data set to figure out their exact relationships). Is the presence of 100 ancient human skeletons consistent with your model? Yes. Is your inability to identify their exact relationship a weakness of your model? No.

Likewise, is the presence of fossil hominids with both human and non-human ape morphological features consistent with evolutionary theory? Yes. Is our inability to arrange them in a unique phylogeny a weakness of the theory? No. It simply stems from necessarily insufficient data.

[otseng]

Please show evidence of fire being in use in the last million years.

There's quite a bit of evidence:

I think stating that there's "quite a bit of evidence" is overstating your case.

Evolution of Fire

The use of fire has long been thought to have coincided with, and perhaps aided in the precipitation of, the evolution of modern human culture and language around forty thousand years ago. That is, up until last year, when two controversial studies were released that brought this long held notion into question. These new findings suggest that not only might fire have been put to intentional use by humans as far back as 1.6 million years ...
[...]
Last April, this question was answered by Brian Ludwig of Rutgers University.
After studying forty thousand pieces of flint tool artifacts, ranging from 1 to 2.5 million years old, from sites throughout Africa, Ludwig found some surprising results. When rocks have been exposed to heat, they develop telltale signs of heat exposure, in the form of observable “potlid fractures�. After studying his tool artifacts, Ludwig discovered that the artifacts he was studying started to show these small fractures only after about 1.6 million years (McCrone, 2000). This finding suggests that by that time, H. erectus was not only using campfires regularly, but also hunting and possibly even cooking tools.
[...]

Tools older than 1.7 million years ago would be Mode One tools, which consist of stone pebble tools. If flint tool artifacts were found older than this, it would not fit into the normal tool evolutionary timeframe.

Also, the supposed "potlid fractures" would not be any hard evidence of fire use. First, why would flint tool artifacts be placed in fire? Especially since Acheulean (biface) tools were not hafted? And they could also have been heated by natural fires. Or fractures could be from their normal wear and tear, rather than by fire.

Human evolution, fire, and food

... In spite of the fact fire use becomes spottier the farther back in the historical record you go, Wringham maintains that this clutch tool could have triggered the cascade. In fact, it is interesting to note that evidence for the use of fire –spotty though it may be- goes as far back as 1.6 millions years to about the time H.erectus appeared.
[...]

Yes, spotty though it may be.

Also, I currently believe that H.erectus were human (though I do not hold that they existed millions of years ago). So, equating H.erectus with fire would not be out of the question for me.

Did homo erectus discover fire?

The homo sapiens mental revolution took place between 100,000 and 40,000 years ago, following the development of grammatical speech. But Homo erectus was pretty smart already judging by evidence that fire had been discovered over 1.6 million years ago. Could fire really have been such an early discovery?
[...]
New evidence, however, suggests that human exploitation of fire may be quite incredibly ancient, going back some 1.6 million years. Recently developed forensic techniques are strengthening the case that some long-disputed fire remains found in Kenya, East Africa, were indeed kindled by our ancestors.
[...]
At both sites, archaeologists found the bones and stone tools of Homo erectus--the first hominid species to have a markedly larger brain and fully human-proportioned body. At Koobi Fora, the excavations also uncovered a scattering of ten small, half-metre diameter, "lenses" of baked orange earth dating to around 1.6 million years ago.
[...]

Another interesting quote from your source:

Within palaeoanthropological circles, there will be many fingers crossed hoping the latest findings just aren’t true. This is because hominid control of fire at 1.6 million years poses huge problems for current thinking about human evolution. The story goes that technologically sophisticated humans arrived with a "big bang" only about 40 000 years ago, with the development of grammatical speech. If the very early date for the control of fire holds up, then either we have to believe that kindling a roaring blaze is essentially--indeed literally--a pretty dumb skill. Or else we must be willing to upgrade the mental abilities of our forebears rather considerably.

[GrumpyMrGruff]

However, the question is what can explain that all other female lines disappeared? In terms of the probability that only one female is the progenitor of all, I'm going to ask Zeeby in my next post about that.

As Zeeby pointed out, in stochastic birth-death models like this the number of progeny left by each member of the initial population will inevitably go to zero or one after a sufficient amount of time (dependent on model parameters). The correct question is not if one female's offspring will eventually dominate the population, but how long (on average) it will take for this to occur. To answer that question, we need to know things like population structure, generation time, population size, etc.

Haplogroup A is not limited to Africa.

Haplogroup A is found mainly in the Southern Nile region and Southern Africa. However, at lower frequencies, M91 is found in many areas of Africa, including Morocco, Egypt, and Cameroon. Outside of Africa, it has been detected in European males in England, Portugal, the Mediterranean islands of Sardinia, Italy, and Lesbos, Greece, and the Eastern Mediterranean regions of Anatolia, the Levant, and Southern Arabia.

http://en.wikipedia.org/wiki/Haplogroup_A_%28Y-DNA%29

True. You know what they say about sailors: A girl in every port. Mediterranean, coastal Atlantic, and over-land trade (including Mideast and African slave trade) dates back thousands of years, at least to the Phoenicians. There was doubtless some gene flow between these populations. However, the majority of living haplogroup A members live in Africa (all figures adapted from 23andme.com unless otherwise noted):


Figure 1: Haplogroup A Biogeography Circa 1500 (Before Modern International Transit)

For Haplogroup BT, it is a hypothetical grouping and no human actually has a BT Y-chromosome. Same also goes for CT and CF.

It would be correct to say that nobody sampled has the BT*, CT*, or CF* haplotype. Conversely, greater than 90% of the world has the mutational markers that denote the BT haplogroup. What does this mean? The asterisk denotes an ancestral state. Consider the following examples.


Figure 2: Representing Ancestral States in the Y-Chromosomal Phylogeny

No sampled individuals are BT*, but all members of haplogroups B, D/E, C, and F share the mutations of the inferred ancestor BT... plus additional mutations. Is the ancestor BT hypothetical? Sure, the same way yAdam is hypothetical. The data makes a compelling case that a BT population existed, even if it did not survive to modern times.

The same goes for CT*. Haplogroups D/E, C, and F all share common mutations originally present in inferred ancestral CT... plus additional defining mutations. Saying that there is no CT* simply means that no sampled individuals possess this defining set of mutations minus the further mutations found in D/E, C, and F.

A similar pattern is present in CF.

Conversely, F* and D/E* both denote living individuals with the inferred ancestral states... minus additional defining mutations of the F and D/E subtypes. In general, because birth-death processes inevitably cause the loss of some lineages, it is more likely to find such living ancestors if the ancestors lived recently. Hence, it makes sense that we find surviving examples of more recent ancestors like F* or D/E* or K* rather than more ancient ancestors like BT* or CT* or yAdam*.

Also there is no definitive place of origin for BT either, though sources say that it probably originated in North East Africa.

Haplogroup BT split off from haplogroup A 70,000 years bp , probably originating in North East Africa from Y-chromosomal Adam. It contains all living human Y-DNA haplogroups except for A.

http://en.wikipedia.org/wiki/Haplogroup_BT_%28Y-DNA%29

Yet if you map majority biogeography onto the phylogeny (as shown in the wiki page you link to), an interesting trend emerges.


Figure 3: Comparing Biogeography and Phylogeny of Y-Chromosomal Haplogroups (Wikimedia Commons)

In agreement with the mtDNA phylogeny I presented previously, maximum parsimony (i.e., minimum number of migrations) suggests two migrations out of Africa. Note that D/E exists both in both Africa and Eurasia, but consider its distribution:


Figure 4: Haplogroup D/E Biogeography Circa 1500

It has a much higher density within Africa, suggesting that Eurasian populations represent migrations from Africa to Eurasia.

Likewise, haplogroup B is almost exclusively African. So far, this is all consistent with the Wikimedia phylogeny and the mtDNA phylogeny.


Figure 5: Haplogroup B Biogeography Circa 1500

The F Haplogroup contains more than 90% of the world's population.

In human genetics, haplogroup F or FT is an enormous Y-chromosome haplogroup spanning all the continents. This haplogroup and its subclades contain more than 90% of the world's existing male population.

http://en.wikipedia.org/wiki/Haplogroup_F_%28Y-DNA%29

Yep, most Eurasians are. I'm a member of F. Specifically, G2a. I don't feel special at all.

Haplogroups C and F looks like this, by the way:


Figure 6: Haplogroup C Biogeography Circa 1500


Figure 7: Haplogroup F Biogeography Circa 1500

Note the limited penetration into Africa, consistent with the out-of-Africa migration predating CF as denoted in Figure 3.

It is theorized that it originated in the Middle East area.

Well, somewhere ranging between the Mideast and India, anyway.

Because BT, CT, and CF are all hypothetical and not found in any human, it is entirely possible that F can be located nearer to the root of the tree.

You lost me here. This sounds like a non sequitur. yAdam is hypothetical in exactly the same way that BT, CT, and CF are hypothetical: Their markers, though shared by many males (the default marker set in the case of yAdam) are not found in isolation in any living male.

Quite the contrary: The existence of an inferred ancestral haplotype (e.g., F*) in a living sample suggests that the ancestor lived more recently. The more ancient the ancestor (and the closer to the root of the tree), the more likely random genetic drift would wipe out the uniquely ancestral population.

And since it accounts for 90% of the current population, this would make it seem more likely that it is close to the root.

This statement ignores the important fact that we cannot assume identical birth and mortality rates for all populations (dependent on environment and lifestyle). This might be a valid extrapolation if we assumed lockstep reproduction for all humans and ignored both phylogenetic and biogeographical evidence.

The root of the tree is not chosen arbitrarily. The tree is rooted on the longest branch. What does this mean? The phylogenetic analysis sets branch length proportional to amount of change between samples. As I previously noted, the branching pattern of mtDNA and y-chromosomal lineages is parsimoniously explained by diverging migrations of mostly non-interbreeding human populations. Assuming that these mutations accumulate at similar rates on average (typical in the absence of selective pressures), the samples at either end of the longest branch would represent the most ancient divergence of migratory populations. Where should we place yAdam (the root) in the tree? The longest branch. Why? He had to predate the most ancient migratory split if both divergent populations (and all subsequent human populations) inherited his y-chromosome.


Figure 8: Rooting the Tree: The Longest Branch Method

Imagine that this tree is unrooted. Every branch sticks out radially, looking something like this sketch. Assuming the mutations in question are neutral, we can root the tree by looking at the length of the branches. Without yAdam (the root), the branch BT-to-A has length (alpha+beta). This is longer than any other branch - the next longest is BT-to-B with a length of (gamma+delta+epsilon). All other branches are shorter still. Hence, yAdam is placed on A-to-BT. The A populations are more distant genetically from other samples than any other samples are from one another. This indicates that the divergence of A and all other samples is the most ancient migratory split.

So, though this is tentative for now, it's possible to arrange the Y-chromosome tree into 3 descendants off of a common ancestor: AB, CF, and DE.

Upon inspection this tree presents a major problem. Phylogenetic analysis suggests that B is more closely related to D/E, C, and F than it is to A. Your creation of an AB most recent common ancestor is at odds with the genetic data. Aside from being wrong (insofar as it contradicts data), the root of this tree could be placed in either Africa or Eurasia. It doesn't do much to advance your case for a Eurasian origin.

If the only features we could compare were morphological, there might be cause for confusion (since different sequences can sometimes encode similar structures).

Then the use of fossil evidence would be unreliable.

This is why fossil evidence represents necessarily insufficient data set for unique phylogeny determination, yes.

Note that every phylogenetic tree we make assumes homology.

Would even phylogenetic trees based on genetics also assume homology?

Yes. There are different methods, but in general they arrange the sequences so that same mutations don't have to occur over and over again (an unlikely event). In other words, they assign similar sequences a more recent common ancestor than dissimilar sequences because their similarity is most parsimoniously accounted for by an ancestor that possessed their shared traits. As I've said, this is not the interesting part. The interesting part is that new sets sequences from from same set of organisms yield the same tree when you apply this method. This is what's predicted in new data if mutation and natural selection are driving the process, but this pattern is not accounted for a priori by design models. Creationists must apply a post hoc, non-mechanistic explanation that 'the designer could've built them this way' (unfalsifiable). How couldn't the designer have done it?

simply show that different genes from the same set of organisms infer the same tree no more often than randomized trees.

OK, let's spend some more time on this then.

If different genes from the same organisms point to different evolutionary pathways, these would be different trees correct?
What would constitute randomized trees?

I am waiting on a phylogenetics textbook I ordered this week. Until it arrives, I will only be able to proceed off of class notes from a phylogenetics course I took a few years ago. With your permission, I'd like to get my references together before I go into this in detail.

In terms of the mechanism that a species is designed, it not necessary to know how something is designed to posit a designer.

Ultimately, the scientific method is used to ask and answer "How?" Invoking design does not answer how a designer did anything, and we cannot make falsifiable predictions about new data without determining what physical characteristics arise from the design process. Remember, predictions come in the form: 'New data I acquire should have the patterns ABC if they were caused by Mechanisms XYZ.' Falsification criteria come in the form: 'Mechanisms XYZ are incosistent and/or insufficient to cause the patterns DEF; if we see DEF, XYZ are wrong/insufficient.'

Mutation, drift and natural selection can predict consistent patterns and inconsistent patterns. Invoking 'design' as a mechanism does not allow us to identify either.

One example would be the SETI program. If researchers find a signal from another planet, it would not be immediately rejected because they do not know how an alien civilization created the signal.

On the contrary, SETI made strong assumptions about the mechanisms used by ETIs: They assumed any intelligence-based broadcasts would be produced by frequency or amplitude modulation of EM waves (radio, microwave, etc.). These are the types of signals they listened for. If ETIs exist and use other methods of encoding information, SETI (because of its assumptions about how ETIs created their signals) would have missed them.

Further, an apparently intelligent source for a signal cannot be practically falsified or confirmed in most cases. Sometimes a natural phenomenon provides a more parsimonious answer, but the only way to confirm ETI sources for signals would be to attempt back-and-forth communication (likely impossible due to distance and conceptual barriers) or attempt to sample the source directly (likely impossible due to distance).

As a sci-fi nerd, I love the idea of SETI. As a scientist, I think it was a questionable investment at best. It attempts to address a question that seems practically unfalsifiable in most cases (even if it is falsifiable in principle).

[SailingCyclops]

Sometimes a natural phenomenon provides a more parsimonious answer, but the only way to confirm ETI sources for signals would be to attempt back-and-forth communication (likely impossible due to distance and conceptual barriers) or attempt to sample the source directly (likely impossible due to distance).

As a sci-fi nerd, I love the idea of SETI. As a scientist, I think it was a questionable investment at best. It attempts to address a question that seems practically unfalsifiable in most cases (even if it is falsifiable in principle).

Unless of course the ETI was intentionally transmitting a signal intended to be understood by other technological civilizations as originating from intelligence. Such a transmission could be as simple as a set of prime numbers being sent as frequency modulated tones. Receiving such would certainly rule out natural causes. I know of no quasar which could mimic a prime number em burst.

Bob

[GrumpyMrGruff]

Important correction to my previous post:

The root for the y-chromosomal phylogeny was performed by outgroup comparison with homologous regions of the chimpanzee y-chromosome according to this white paper.[1]

I was under the impression that it was rooted according to a molecular clock assumption. My bad; I should have double checked.

[GrumpyMrGruff]

Unless of course the ETI was intentionally transmitting a signal intended to be understood by other technological civilizations as originating from intelligence. Such a transmission could be as simple as a set of prime numbers being sent as frequency modulated tones. Receiving such would certainly rule out natural causes. I know of no quasar which could mimic a prime number em burst.

Bob

I agree that we would flag a prime number signal as potential ETI because a) we know of no astronomical phenomena that produce such transmissions and b) we can produce them ourselves. My contention is that having intercepted such a signal, there are no practical ways to verify or rule out an ETI source (with a few exceptions if the source is exceptionally nearby).