Mutation Rate in Humans Has Slowed Down

I am not quite sure what this means, yet. Researchers at the Aarhus University, Denmark, and the Copenhagen Zoo have discovered that, when compared to our nearest taxonomic relatives, our mutation rates have slowed down. Science Daily has the scoop:

"Over the past six years, several large studies have done this for humans, so we have extensive knowledge about the number of new mutations that occur in humans every year. Until now, however, there have not been any good estimates of mutation rates in our closest primate relatives," says Søren Besenbacher from Aarhus University.

The study has looked at ten families with father, mother and offspring: seven chimpanzee-families, two gorilla families and one orangutan family. In all the families, researchers found more mutations than would be expected on the basis of the number of mutations that would typically arise in human families with parents of similar age. This means that the annual mutation rate is now about one-third lower in humans than in apes.

Why is this important for the study of human origins?

The higher rates in apes have an impact on the length of time estimated to have passed since the common ancestor of humans and chimpanzees lived. This is because a higher mutation rate means that the number of genetic differences between humans and chimpanzees will accumulate over a shorter period.

If the new mutation rates for apes are applied, the researchers estimate that the species formation (speciation) that separated humans from chimpanzees took place around 6.6 million years ago. If the mutation rate for humans is applied, speciation should have been around 10 million years ago.

The six-to-eight million year point for the LCA never made a whole lot of sense to me. If the fossil material from Orrorin, at 6 mya really does reflect bipedality, then the split has to have been much earlier.  The material from Ardipithecus kadabba is very sketchy with regard to bipedalism (one toe bone found ten miles away), but the fragmentary post-cranial bones can be confidently identified as being hominin, in nature.  Furthermore, the fossil material is dated to between 5.6 and 5.8 mya.  That would leave a very short period of time.  It cannot be pre-split because the fossil material exhibits derivations in the hominin direction, rather than the modern ape direction. 

If this study holds up, it will change how we view the search for the LCA. 

Did the LCA Have Teeth More Like a Gorilla?

Artificial intelligence is playing a role in understanding human evolution.  From the Australian site News.com comes a story about new work in trying to understand what the last common ancestor to apes and humans might have looked like:

IT’S an image imprinted on our brains: the steady march of evolution from chimp to human. But it’s not quite right.

Monkeys don’t belong on the tree. They have tails.

Chimps, which don’t, are with Bonobos our closest living relatives. And, as such, both should be standing alongside us in the march of life.

Stretching out behind should be a gradually converging branch of earlier variations.

Ultimately, between six and eight million years ago, the branches almost certainly converge on one common ancestor.

We know almost nothing about what that was.

We have reasonably secure evidence of bipedality at around 6 million years in the form of Orrorin tugenensis from Kenya, as well as a crushed skull from Chad called Sahelanthropus that may or may not be 7 million years old, and recently, fossil footprints, purporting to show bipedal walking, from Crete have been uncovered that have been dated to around 5.7 million years ago.  Beyond that, nothing.  That is where the new AI study comes in.

The researchers used machine learning to teach an artificial intelligence to identify and classify fossilised hominid teeth dating from 25 million years ago. It then sifted through these to find patterns of development.

The study published in the science journal PaleoBios found one tantalising tip.

Our common ancestor almost certainly had gorilla-like teeth.

Now, it’s not a lot. And it certainly doesn’t say our ancestor was a gorilla.

But what it does do is add some shape and substance to this nebulous period of our human origins.

The information that is contained in the article is not nearly as cut and dried as is indicated by the news story. From the conclusion:

Given that the divergence of humans and chimpanzees occurred in the late Miocene, and that Miocene apes are much more similar to Gorilla in dental proportions, we assert that gorillas are the more appropriate extant model for the African ape LCA in terms of the relative sizes of the postcanine teeth. This similarity in dental proportions likely has implications for the interpretation of dietary adaptation and possibly phylogenetic relationships in Miocene apes, including the chimpanzee-human last common ancestor.

What this likely means is that, during the Miocene, which was the golden age of the apes, even after the divergence of Gorillas from the main line, there were extant forms that continued to have varying degrees of traits that could be associated with gorillas, presenting a classic case of collateral ancestry.  It is possible that one of the lines eventually led to chimpanzees, while another led to us.  We won't know more until we actually have some fossil remains from that missing time period. 
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Ardipithecus May Not Have Been Entirely a Facultative Biped After All

In a new article in the Proceedings of the National Academy of Sciences, several researchers have concluded, using 3D morphometric analysis have discovered that Ardipithecus ramidus, while still having facultative (didn't have to but could) bipedalism, when it did walk, its bipedal gait was nearly human.  From the abstract:

We show that hamstring-powered hip extension during habitual walking and climbing in living apes and humans is strongly predicted, and likely constrained, by the relative length and orientation of the ischium. Ape pelves permit greater extensor moments at the hip, enhancing climbing capability, but limit their range of hip extension, resulting in a crouched gait. Human pelves reduce hip extensor moments but permit a greater degree of hip extension, which greatly improves walking economy (i.e., distance traveled/energy consumed). Applying these results to fossil pelves suggests that early hominins differed from both humans and extant apes in having an economical walking gait without sacrificing climbing capability. Ardipithecus was capable of nearly human-like hip extension during bipedal walking, but retained the capacity for powerful, ape-like hip extension during vertical climbing. Hip extension capability was essentially human-like in Australopithecus afarensis and Australopithecus africanus, suggesting an economical walking gait but reduced mechanical advantage for powered hip extension during climbing.

This positions Ardipithecus as the classic intermediate in terms of bipedal locomotion.Although there are many traits in Australopithecus afarensis that are still transitional in terms of the rib cage, dentition and aspects of the hip, it is clear that the major adaptations for bipedalism were in place nearly a million years earlier.  This also suggests that it is not out of the realm of possibility that the fossil footprints in Crete really do reflect a bipedal hominin.  At the risk of positing heresy, the fact remains that we really don't know exactly where hominins first appeared.  This study also reinforced the distinct separation between apes and humans in terms of iliac shape, and that this split must have taken place even further back in time that we have supposed.

The Independent has a news story on this here.  One of the authors, Herman Pontzer remarks:

“It kicks us out of this old paradigm of thinking about human evolution,”...“In that old picture that is everywhere where you have the evolution of man going from crouching thing to upright thing to a human – as much as we have known that is not right, I still think people have it in their heads.”

Elizabeth Mitchell, Homo naledi and the Straw Man

Elizabeth Mitchell, of Answers in Genesis, has written the rebuttal to the eLife Science paper on the new hominin find from South Africa, Homo naledi.  Sadly, her opening premise suffers from a fatal logical error, and all that follows proceeds from this premise. She writes:

Berger’s team believes the bones paint a mosaic picture of a species mixing human-like “Homo” and australopithecine ape features. Composites constructed from four partial skulls in the assemblage have small brain capacities—560 cc and 465 cc—that overlap the usual brain capacities of australopithecines. Such braincases are much smaller than those seen in most archaic humans1 and less than half the average for modern humans.

Hidden in this paragraph is a theme which runs throughout the post: that australopithecines were apes.  Compare, for example, these passages.  First, what Berger et al. write about the shoulder girdle:

The shoulders are configured largely like those of australopiths. The vertebrae are most similar to Pleistocene members of the genus Homo, whereas the ribcage is wide distally like Au. afarensis.

Now, what Mitchell writes:

Homo naledi’s shoulder joints and curved finger bones are typical of tree-swinging apes. Its flared hips are typical of australopithecine apes. The lower ribcage widens just like the ribcage of australopithecine apes.

When Raymond Dart discovered the first australopithecine specimen, in 1924, the first thing he noticed was that

it was not an ape.

As I wrote in more detailed fashion here, the find had several characteristics simply not found on any ape. First, the foramen magnum, the hole through which the spinal cord exits the head, was not at the back of the head, as in apes, but was on the bottom of the skull. Second, the teeth were not those of an ape, but had the dimensions of human teeth. In apes, even infant apes, the canines extend beyond the tooth row. In this skull, they did not. Third, the skull was simply too large to be that of an infant ape, based on the development. Fourth, there had never been found any apes in South Africa. Dart was a good anatomist and knew that what he had was not quite human—the skull was too small for that and the front of the face was too ape-like, but he also knew he did not have an ape.  That is why Dart gave it the name he did: Australopithecus africanus, “Southern Ape-Man from Africa.”   

Since this discovery some ninety one years ago,  the validity of this genus has only been reinforced, with the additional discoveries of more than ten different species of Australopithecus, all with variations on the same theme, and all with the following non-ape characteristics:

• human-like teeth (although quite large in some species)
• modern double-s shaped vertebral column
• short, wide hips that resemble humans and not apes
• a valgus knee, with the femoral-tibial articulation at an angle, instead of straight up, as in apes
• a laterally-bending proximal femur to accomodate the wide hips and the connexion to the tibia and
• a modern gait (reflected in preserved 3.6 million year old footprints at Laetoli)

There are countless other small anatomical characteristics that separate apes from these early hominins but the ones outlined above are enough to demonstrate that the initial premise of Dr. Mitchell is, simply, incorrect.

But there is something deeper at work here.  Pick up a paper on australopithecines, any paper, written in the last sixty years and you will find discussions of how these forms differed from each other and, more importantly, how they differ from apes.  Are they human?  Manifestly not.  In some early species, there are characteristics that are, indeed, intermediate between apes and early humans. But even that gives rise to the concept of transitional traits and forms in the fossil record.  That is where the problem lies.  If australopithecines can be painted as apes from the outset, then the task of showing that the new Homo naledi specimen is not different from australopithecines, and therefore, apes, becomes easier.

Then she writes something startling:

The question then is what is Homo naledi? Even the evolutionary anthropologists are not in agreement on that point, though most seem to have jumped on the Homo bandwagon. Yet while the fossil record contains many legitimate examples of extinct varieties of humans, such as Homo erectus and Homo neanderthalensis, after assessing the published reports, we beg to differ with Berger’s assessment of Homo naledi. We do not believe Homo naledi deserves its Homo designation. [Emphasis Mine]

When did they these fossil forms go extinct? There is no evidence of extinction in the accounts in the Bible. Other writers do not seem to think they went extinct during the flood.  David Menton is firm in his conviction that Homo erectus represents a post-Babel population:

Neanderthals buried their dead and may have worn jewelry. Homo erectus seems to have divvied up jobs to prepare food and sailed the high seas. Even with little to go on, we can be fairly certain the Denisovans wore jewelry, and the much-maligned “hobbits” left tools useful for dicing up lunch. All uniquely human traits—traits that show creatures made in the image of God.

Which one of the biblical patriarchs had an angular torus, large brow ridges, thick cranial bones and a cranial capacity of 900 cubic centimeters? All of these traits would have stood out in any population. The variation present that Menton squeezes into one happy family vastly exceeds that present in any other naturally-occurring genus on the planet, let alone species. 

She finishes her post with the same, time and time again rebutted argument that the reason that Homo naledi is not a human is similar to australopithecines and, therefore, is nothing more than an ape.  This is the vacuum chamber/wind tunnel that AiG operates within.  Despite clear, decisive anatomical evidence to the contrary, the writers keep telling themselves that australopithecines were nothing more than apes.  The argument still has no credibility.

BioLogos, Ken Ham and David Menton—A Response, Part IV

This is the fourth part of my response to David Menton's post on human origins.  Links to the first three appear below this post.  Menton continues his ham-fisted, ignorant attack on the human fossil record.

Point 8.  He writes:  

Many apemen are merely apes that evolutionists have attempted to upscale to fill the gap between apes and men. These include all the australopithecines, as well as a host of other extinct apes such as Ardipithecus, Orrorin, Sahelanthropus, and Kenyanthropus. All have obviously ape skulls, ape pelvises, and ape hands and feet. Nevertheless, australopithecines (especially Australopithecus afarensis) are often portrayed as having hands and feet identical to modern man; a ramrod-straight, upright posture; and a human gait.

The best-known specimen of A. afarensis is the fossil commonly known as “Lucy.” A life-like mannequin of “Lucy” in the Living World exhibit at the St. Louis Zoo shows a hairy, humanlike female body with human hands and feet but with an obviously apelike head. The three-foot-tall Lucy stands erect in a deeply pensive pose with her right forefinger curled under her chin, her eyes gazing off into the distance as if she were contemplating the mind of Newton.

Few visitors are aware that this is a gross misrepresentation of what is known about the fossil ape Australopithecus afarensis. These apes are known to be long-armed knuckle-walkers with locking wrists. Both the hands and feet of this creature are clearly apelike. Paleoanthropologists Jack Stern and Randall Sussman2 have reported that the hands of this species are “surprisingly similar to hands found in the small end of the pygmy chimpanzee–common chimpanzee range.” They report that the feet, like the hands, are “long, curved and heavily muscled” much like those of living tree-dwelling primates. The authors conclude that no living primate has such hands and feet “for any purpose other than to meet the demands of full or part-time arboreal (tree-dwelling) life.” 

Some background involving the Miocene apes. At the beginning of the Miocene epoch, apes had largely generalized skeletal structures, with few of the adaptations that we see in the modern apes, or in humans.  Toward the end of the Miocene, biomechanical adaptations are seen in many of the apes.  For example, Oreopithecus has developed a locomotor pattern seen in modern non-human apes (although it was mis-identified by Casey Luskin as bipedal).

Menton, having taken us through the differences between apes and humans, suggests that Ardipithecus, Orrorin, Sahelanthropus and Kenyanthropus all have “obviously ape skulls, ape pelvises, and ape hands and feet.”

Really?

• Kenyanthropus consists of a single skull find that is so badly crushed that most researchers have pretty much written it off as being unusable in taxonomic reconstruction.
• Sahelanthropus is also a single skull find that was also crushed and may, in fact, be a surface find.
• Orrorin tugenensis is a collection of post-cranial remains, the most important of which is a partial femur, which showed clear adaptations toward bipedality. 
• Ardipithecus ramidus consists of both cranial and post-cranial remains, including both hands and feet.  Here is what Owen Lovejoy and colleagues wrote about it in 2009:

“The gluteal muscles had been repositioned so that Ar. Ramidus could walk without shifting its center of mass from side to side. This is made clear not only by the shape of its ilium, but by the appearance of a special growth site unique to hominids among all primates (the anterior inferior iliac spine). However, its lower pelvis was still almost entirely ape-like, presumably because it still had massive hindlimb muscles for active climbing.”

How does Menton describe the locomotion of modern apes?  He writes:

These animals manage to keep their weight over their feet when walking by swinging their body from side to side in the familiar “ape walk.” 

Yet he calls Ardipithecus “merely” an ape. By his own description, Ardipithecus is clearly not “merely” an ape. Did he just miss this detail, or did he simply choose not to include it?

To recap this point,  he writes that all of the finds he mentions have “obviously ape skulls, ape pelvises, and ape hands and feet,” and yet we find that only one of the finds has those body parts preserved.  He, further, ignores critical morphology on the Ardipithecus remains to make it seem as if it has no hominin adaptations.  How are we to believe what he writes when he so incompetently describes the fossils he is denigrating?

Point 9: In quoting Stern and Susman, here, again, Menton picks and chooses what he wants to use and doesn't tell his audience other critical information that undercuts his position.  Menton writes as if Australopithecus afarensis were only an ape, yet Stern and Susman write, in their conclusion:

In our opinion A. afarensis is very close to what can be called a “missing link.” It possesses a combination of traits entirely appropriate for an animal that had traveled well down the road toward full-time bipedality, but which retained structural features that enabled it to use the trees efficiently for feeding, resting, sleeping, or escape. prior to the discovery of the Hadar remains, one could not have predicted precisely what combination of traits would be found in a transitional form such as A. afarensis.

These writers, who, unlike Menton, examined the remains directly, clearly did not conclude it was merely an ape but, in fact, a transitional form between the apes that came before, and the hominins that came after.

But worse, Menton completely ignores other characteristics of A. afarensis that don't just undercut his position that it is merely an ape, they destroy it. 

• The first premolar in apes (or bicuspid if you prefer) is long and rotated toward the front of the mouth. This is so it can constantly sharpen the maxillary canine as the ape bites down. This is known as a "sectorial premolar". In humans, this tooth is rotated so that the cusp division is parallel to the tooth row and does not stick up beyond it. The maxillary canine is, correspondingly, short. In Australopithecus afarensis, this tooth is rotated HALF-WAY and partially sticks up from the tooth row. The canine is shortened as in modern humans.

• The palate of the mouth in apes is shaped like a hard "U" with the back teeth parallel to each other. In humans, the palate is more "V" shaped. In A. afarensis, it is intermediate between these two shapes.

• In apes, there is a distinct space between the canine and the first premolar, called a diastema. In humans, this space is absent. In A. afarensis, a diastema is present but it is remarkably reduced in size over the ape condition.

In other instances, some characteristics are completely ape-like and some are completely human-like. For example:

• The digits (phalanges) on both the hands and feet are curved, as in apes. In humans, they are straight.

• The pelvis is flared (wide from side to side) and short from top to bottom, as in humans.

• The hole in the skull where the spinal chord exits the brain, the foramen magnum, is located on the bottom of the skull in Australopithecus afarensis, as in humans.  Having a hole at the base reflects a bipedal gait.

• the knee joint, which preserves the bottom (distal) section of the femur and the top (proximal) section of the tibia shows that the femur is angled, as in humans. This is the "carrying angle" of which Menton wrote. The A. afarensis position, once again, reflects bipedalism.

These characteristics are exactly what you would expect to find in a transitional species: some characteristics transitional, some ape-like and some human-like. Most of the above information was taken from Lucy: The Beginnings of Humankind and Johanson et al. (1982) but can be found in most textbooks about this subject.  It is amazing that Menton went to no effort to locate this information before dismissing A. afarensis' transitional status without thought.    It is, further, amazing that Ken Ham would hold Menton's post up as being authoritative when it is so badly researched and written.

On to Part V. 

Darwin Was Right

Or at least his grandson was. Apparently, one of the younger Darwin's ideas was that the movement and mixing of water between the equator and poles is influenced by sea life, who swim through the water. This was an idea that was largely ignored until recently. As a report appearing in PhysOrg notes:

Using a combination of theoretical modeling, energy calculations, and field observations, researchers from the California Institute of Technology (Caltech) have for the first time described a mechanism that explains how some of the ocean's tiniest swimming animals can have a huge impact on large-scale ocean mixing.

The idea was largely discarded because it was felt that the movement of the ocean would overwhelm any movement that was made by the fish. Not so, they say:"

Darwin's grandson discovered a mechanism for mixing similar in principle to the idea of drafting in aerodynamics," Dabiri explains. "In this mechanism, an individual organism literally drags the surrounding water with it as it goes."

Using this idea as their basis, Dabiri and Katija did some mathematical simulations of what might happen if you had many small animals all moving at more or less the same time, in the same direction. After all, each day, billions of tiny krill and copepods migrate hundreds of meters from the depths of the ocean toward the surface. Darwin's mechanism would suggest that they drag some of the colder, heavier bottom water up with them toward the warmer, lighter water at the top. This would create instability, and eventually, the water would flip, mixing itself as it went.

This has tremendous implications for evolutionary development. The movement of ocean currents has a large effect on continental temperatures which, in turn, has a large effect on the kinds of vegetation that grow and the kinds of fauna that live there. For example, it is likely that the expansion of the Mediterranean during the Miocene led to cooler temperatures in North Africa, specifically the Afar triangle. This led to reduction in forests and an increase in savannas. A group of late Miocene apes began to exploit the forest fringe area and established their own niche—these became the early hominids. I will be curious to see how this research pans out.


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After All, If You Can't Laugh at Yourself...

The June 4 issue of Current Biology contains a study indicating that laughter goes back beyond the ape-human split. The article, in Thaindian reports:

“This study is the first phylogenetic test of the evolutionary continuity of a human emotional expression,” said Marina Davila Ross of the University of Portsmouth in the United Kingdom.

“It supports the idea that there is laughter in apes,” she added.

To reach the conclusion, researchers analysed the recorded sounds of tickle-induced vocalizations produced by infant and juvenile orangutans, chimpanzees, gorillas, and bonobos, as well as those of human infants. A quantitative phylogenetic analysis of those acoustic data found that the best “tree” to represent the evolutionary relationships among those sounds matched the known evolutionary relationships among the five species based on genetics.

The researchers said that the findings support a common evolutionary origin for the human and ape tickle-induced expressions.They also show that laughter evolved gradually over the last 10 to 16 million years of primate evolutionary history.

But human laughter is nonetheless acoustically distinct from that of great apes and reached that state through an evident exaggeration of pre-existing acoustic features after the hominin separation from ancestors shared with bonobos and chimps, about 4.5 to 6 million years ago, Davila Ross says.

Uh, not 4.5 to 6 mya. Not if Orrorin and Sahelanthropus represent incipient hominids. More like 9 to 10 mya. Still, it is nice to know we share such a stress-reducing behavior.