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dr. dolittle — Tue, 04 Nov 2014 22:16:24 +0000

Your vote needed!!

Just in case you felt like casting a vote for a cute and cuddly cause, the Phoenix Zoo is asking for help in naming a new baby Bornean orangutan. He was born on September 2, 2014 to parents Bess and Michael.

You can vote here

Voting ends November 6th and the winning name will be announced at his/her baby shower on the 8th.

Image of baby orangutan from the Phoenix Zoo
www.phoenixzoo.org

dr. dolittle Tue, 11/04/2014 - 17:16

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The Red Ape Returns & Willi Hennig Superstar!

razib — Thu, 18 Jun 2009 07:17:39 +0000

The Red Ape Returns & Willi Hennig Superstar!

20 years ago Jeffrey Schwartz published The Red Ape, making the case that humanity's closest extant relatives within the animal kingdom were orangutans, not chimpanzees. This was contemporaneous with the media hullabaloo around African Eve, so either you could say that Schwartz's timing was perfect, or it was disastrous. Certainly he was swimming against the spirit of the age, and I recall assuming that The Red Ape was a piece of crankery when I first heard about it, its thesis was so outrageous. But historically the idea that humanity descends from Asian apes is less anomalous, and many scientists of Charles Darwin's time did not agree with his model of an African origin for humanity. The skepticism of this idea persisted deep into the 20th century, one reason that Raymond Dart's discovery of Australopithecus africanus was met with less interest than we might assume. Only with further discoveries of numerous early hominids in East Africa by luminaries such as Richard Leaky and Donald Johanson did our probabilistic framework shift so that the unearthing of a wide range of extinct African apes elicit excitement. After all, one of these (or many) are likely to be the possible precursor to the most important species which walks the earth!

But Jeffrey Schwartz is not deterred, and continues to throw stones at the idols of the age. A few years ago he came out with a second issue of The Red Ape. Today I noticed that he has also coauthored a new paper putting forward the model that orangutans are our closest relatives, Evolution of the second orangutan: phylogeny and biogeography of hominid origins:

Our analyses support the following hypotheses: (1) the living largebodied hominoids represent a monophyletic group comprising two sister clades: humans + orangutans, and chimpanzees (including bonobos) + gorillas (collectively, the African apes); and (2) the human–orangutan clade (dental hominoids) includes fossil hominids (Homo, australopiths, Orrorin) and the Miocene-age apes Hispanopithecus, Ouranopithecus, Ankarapithecus, Sivapithecus, Lufengpithecus, Khoratpithecus and Gigantopithecus (also Plio-Pleistocene of eastern Asia). We also demonstrate that the distributions of living and fossil genera are largely vicariant, with nodes of geographical overlap or proximity between Gigantopithecus and Sivapithecus in Central Asia, and between Pongo, Gigantopithecus, Lufengpithecus and Khoratpithecus in East Asia. The main massing is represented by five genera and eight species in East Asia. The dental hominoid track is spatially correlated with the East African Rift System (EARS) and the Tethys Orogenic Collage (TOC).

Monophyletic simply means that of the set of terminal branches all descend from a common ancestral node. To the left you see the blue highlighting a monophyletic clade: reptiles + birds. Reptiles themselves are not monophyletic, because the class excludes birds, who are descended from the common ancestor of all reptiles. In fact, birds cluster together with crocodiles, alligators, etc., as a monophyletic clade! We don't need molecular biology to know this, it is clear from morphological characters, and has long been so. In fact that's why the hypothesis emerged and became dominant that birds are the last extant lineage of theropod dinosaurs long before the rise of molecular techniques (birds can be shown to be closely related to crocodiles even without the extraction of biological material from fossils).

Though most people do not know what a monophyletic lineage is, the intuition that chimpanzees are our closet relatives in the animal world has sunk deep into the public consciousness. So deeply that Jared Diamond wrote a book which was titled The Third Chimpanzee, implying that humans should be viewed as the third chimpanzee species after the common chimp and the bonobo. The use of these two species as analogs to our own lineage has resulted in warring conceptions of human nature. The authors of The Demonic Males looked to common chimps as an echo of the human ancestor and primal condition, while others suggest bonobos might tell us more. Focusing on orangutans would change the whole playing field and upturn a great deal of reasoning which is predicated on our closer connection to chimpanzees (as well as gorillas).

Figure 2a from the paper, to the left, illustrates the main result. I'm not showing you the rest because it relates to Miocene apes and such which I don't know much about. When it comes to fossils Kambiz Kamrani or John Hawks might add some value, but I certainly won't. The way the cladogram was generated is pretty easy to communicate though, they just looked as informative morphological characters (e.g., teeth) and used cladistic methods to generate the most parsimonious tree. The principle of parismony is of course smiled upon in science, and in the context of cladistics what you are trying to explain are synapomorphies, shared derived traits.That is, traits which two lineages exhibit because of common descent, but which other lineages do not because they do not share common descent from the ancestor which originated that trait. Not all traits are created equal when it comes to giving us information which allows one to distinguish between clusters of species which form clades, who we presume emerged over evolutionary time in a contingent manner.

Cladists are almost messianic in their zeal for synapomorphies. There's a reason. A phylogeneticist who collaborated with Allan Wilson's group during the early years of molecular evolution once explained to me that before the cladistic paradigm came to the fore systematics was a total mess with no common currency. Sometimes it was an entertaining mess, such as Ernst Haeckel's famous diagrams, and sometimes an authoritative mess as evidenced by Ernst Mayer's attempts at evolutionary systematics. But arguments always ended with "I said so!" How exactly could one objectively discern right from wrong when intuition ruled the day? Enter Willi Hennig and the cladist revolution, which introduced a genuine system to systematics, so to speak. Using Karl Popper's criterion of falsification and the principle of parsimony a process emerged to clear out the debris of opinion which riddled taxonomy. Modern phylogenetics was born, and the basic ideas were also applied in a molecular context (though from the beginning molecular biologists did not always rely on cladist frameworks, as noted by Schwartz in this paper, nor do they today).

At this point I'll interject something personal. A good friend of mine was trained as a taxonomist, and she told me once that one of the members of her group gave a presentation which did not hue to the strict cladist line. After the talk a cladist approached her privately and berated her for not using "strict Popperian methods." The point here is not the substance but the style. Hennig's ideas added a great deal of rigor and precision, but many people feel that they go too far, and confuse Karl Popper's philosophy of science with science itself. My friend was predominantly a cladist, but her attitude was that there are more things in heaven and earth than only synapomorphies. Taxonomy needed some boundaries in the 20th century, but some cladists are strangling good science in the name of a straightjacket framework.

Jeffrey Schwartz's fixation on morphological characters and dismissal of the sometimes ad hoc and philosophically sloppy molecular methods strikes me as exhibiting this sort of narrowness. The main reason that molecular phylogenetics is viewed as authoritative in evolutionary paleontology is that in the 1970s the fossils and the molecules disagreed, and in the 1980s the fossils came into line with the molecules. There simply aren't that many fossils, and in previous eras the interpretation left much to be desired. With computational methods this is changing, but the reality is that molecular methods in the study of human evolution has withstood the test of time. This simply isn't fleshed out in the paper, which objects to molecular methods in a more general sense.

I don't find Schwartz's objections to the molecular data persuasive. There're the ones I would expect, and I won't go into them because i don't want to get into discussions about the molecular clock and what not. Obviously coalescent theory and such need to be questioned and examined, and models may not be as robust as one would like, but I don't personally find Schwartz's proffered alternative, rejecting most molecular methods as philosophically incoherent, as viable. Morphological characters used in analyses as in the paper above are a small finite subset of the total set of possible characters. In contrast, with the short-term likelihood of a large number of total genomes for both humans and other primates, and computational power to analyzes those genomes, there won't be the problem of methodological bias in terms of characters which are selected for analysis.

I think it is actually of interest to see how human traits and specific genes do not map onto the affinities of total genome content across taxa. In fact, it is interesting to see how this works within human populations. After all, the darkest skinned populations in the world, those of India, Melanesia and Africa, are not a monophyletic group. Rather, Indians and Melanesians cluster with non-Africans generally, light or dark. This is a trivial example, but illustrates that characters which do not map onto general phylogenies are significant and may tell us a great deal of & about the nature of adaptation. My attitude toward the "Red Ape Hypothesis" was that though I dismissed the model I thought the collection of traits where humans resembled orangutans were of interest, note and worthy of further exploration. As it is, Schwartz seems intent on overturning the credibility of molecular systematics itself to stack the odds in favor of his ideas about the origins of humanity. I wouldn't take that bet personally. This might not rank with Fred Hoyle's stubborn adherence to Steady State Theory, but I think the same basic issues are at work. When it comes to models of molecular evolution, mend it, don't end it. We need a diversity of methods, and for many questions fossils offer no answers because of the
small number of remains. The issues relating to this paper are worthwhile because putting a spotlight on the characteristics which can't be predicted by shared descent is going to tell us a lot about evolution, especially adaptation. But these sorts of really radical revisionisms shouldn't lead us to dismissing the traits outside of the main trendline; and yes, genetic sequences are traits too.

Related: For a more detailed review of the paper itself, see The New Scientist.

Note: It seems that to some extent ancient DNA might be a check on some of the molecular evolutionary models which Schwartz contends are not falsifiable.

Cite: Journal of Biogeography (J. Biogeogr.) (2009), Evolution of the second orangutan: phylogeny and biogeography of hominid origins, John R. Grehan and Jeffrey H. Schwartz,

razib Thu, 06/18/2009 - 03:17

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Good post, Razib. There really seems to be an increasing synthesis between molecular/genetic studies and paleontology (with some developmental stuff thrown in to boot). No one discipline holds all the answers, but what is found in one can be tested with discoveries in another. Another example is the status of whales as derived artiodactyls. That's what the molecular studies said, but paleontologists disagreed until they found evidence that confirmed the hypotheses made from proteins. As I said, it is not so much about fossils being better than genes, but using both to test hypotheses.

science = debate.
The history of science shows many cases where the minority opinion turned out to be correct. We need more data, not more flame.

Dr. Schwartz gave a talk here at WVU last earlier this year. I and another professor asked him questions regarding his conclusions and his opinions on molecular methods. While he ended up talking for nearly 20 minutes, he either never answered the questions posed or gave answers that clearly demonstrated that he didn't have a clue what he was talking about with regard to molecular genetic analyses. It was both frustrating and disappointing. Afterwards, I had dinner with him and even gave him a ride to and from the restaurant. During that time, I continued asking questions. Unfortunately, I believe that he has already decided what he wants the answer to his question to be and will only consider data that supports it. Hence (I suspect), his dismissal of molecular data for ungrounded reasons. This isn't good science. I even attempted to continue the conversation via e-mail but never got a response.

Dr. Schwartz gave a talk here at WVU last earlier this year. I was in the front row. I and another professor asked him questions regarding his conclusions and his opinions on molecular methods. While he ended up talking for nearly 20 minutes, he either never answered the questions posed or gave answers that clearly demonstrated that he didn't have a clue what he was talking about with regard to molecular genetic analyses. It was both frustrating and disappointing. Afterwards, I had dinner with him and even gave him a ride to and from the restaurant. During that time, I continued asking questions. Unfortunately, I believe that he has already decided what he wants the answer to his question to be and will only consider data that supports it. Hence (I suspect), his dismissal of molecular data for ungrounded reasons. This isn't good science. I even attempted to continue the conversation via e-mail but never got a response.

Thank you so much for sharing this story about the genetic similarities between humans and orangutans with your readers. I'd like to invite you to visit the Orangutan Outreach website to learn more about the crisis facing orangutans in the wild.

As I'm sure you are well aware, orangutans are critically endangered because of rapid deforestation and the expansion of palm oil plantations in Borneo and Sumatra. If nothing is done to protect orangutans, they will be extinct in just a few years.

Visit the Orangutan Outreach website to learn how YOU can make a difference!

Thanks for your time...

Richard Zimmerman
Director, Orangutan Outreach
http://redapes.org
Reach out and save the orangutans!
Facebook Cause: http://causes.com/redapes

The history of science shows many cases where the minority opinion turned out to be correct. We need more data, not more flame

yes, but the vast majority of well accepted, tested and utilized theories are less overturned than extended. it is always possible to turn the world upside down, but the general assumption that it is right side up is what you should go with operationally.

How they can be any more confident that our anatomical similarities are primitive retentions than they are about genetic similarities?

It's been about 10 years now, but I took my Physical Anthro course from Dr. Schwartz as a major at Pittsburgh.

I'm intrigued, but not surprised, to see he is still thoroughly dismissive of new techniques.

TGGP,

One reason that morphological characters are not so great to use for phylogenetic analysis is because of the functional complexes phenomenon. Well, first of all, one has to address the availability bias caused by the features usually utilized, since they tend to come from the most common types of fossil remnants found, primary teeth and skull fragments. The genetic code, in opposition, specifies the entire organism. And as stated before, functional groups of anatomical features also tend to evolve together; one such example would be the size of the mandible and anterior dentition in Australopithecus. Another functional group might be brain size, cranial length, breadth, height in hominins. Convergent evolution happens more often than you might think; A. aethiopicus ("Black Skull") and A. boisei both have large cheek teeth associated with heavy chewing of low-quality foodstuffs, and cladistic analysis of that singular trait would place them in a monophyletic group, but using other non-associated traits leads many to believe they are actually paraphyletic cousins. Yet another problem with using morphological features is the need to map qualitative anatomical descriptions to quantitative ones for fine-grained work.

I'm a fish taxonomist; long been a classical morphoologist. But I now think, all being equal, that an analysis of DNA morphology is more likely to approach the One True Tree than a classical morphology analysis. First, it is the DNA which is actually transmitted from generation to generation, so a correct analysis of DNA history is as good as it can get. Secondly, classical morphology is DNA seen through a glass darkly. It is influenced by a number of non-geneological factors, and thus reflects more than relationship.

In the killifish family Rivulidae, there have been two independent DNA trees, and one classical norphology tree generated. The DNA trees are remarkably similar, but there is disagreement with the morphological tree in one area. The DNA trees agree on a lineage which includes fishes which have remarkably diverse morphology. The morphology tree spreads these species around as their morphology suggests. The DNA trees have these species on very long branches within their monophyletic lineage. This suggests to me that diversification in this lineage has proceeded a a very rapid rate in comparison with other lineages in the family. So, if this group is indeed monophyletic, its members have diversified so much that classical morphology does not reveal their true relationship.

TGGP,

I've read the Red Ape, and I agree with David, Schwartz does not understand molecular methods. I'm not sure if it's fair to equate him with typical cladists - I think the latter usually understand the methods but impose unreasonable (to the rest of us) philosophical constraints on the analyses. They don't object to all molecular methods, there are plenty of molecular papers in Cladistics after all.

One of the main complaints of the authors seems to be sequence alignment, but let's say you are looking at chimp-human protein sequences, you won't get too many issues with gaps and you are not going to need to do structural alignment.

Thanks for saying it better than I could, Billare.

Great review and critique Razib. I've linked to it here.

But if you teach an Ape to fish…

esiegel — Mon, 12 May 2008 09:26:29 +0000

But if you teach an Ape to fish…

What the heck has this world come to? All over the internet, this picture of an Orangutan trying to fish with a stick has been shown:

But what's the story behind this? Is this evidence that humans are not unique among the Great Apes as tool-users?

Not quite. According to the Daily Mail, this is an orangutan that had extensive exposure to humans; this jungle setting is actually where they reintroduce orangutans into the wild from zoos, private homes and (yikes) butcher shops. This particular orangutan actually doesn't successfully know how to fish; this was something he copied from nearby humans who tangled a stick in with their fishing lines to reel in fish. He would go to the fishermen's site and steal some of their fish using a stick while they were away. Here he (unsuccessfully) attempts to apply this technique on his own. It doesn't work without the fishermen and their fishing lines, though.

What's very interesting about this is that the oldest tools are about 2.5 million years old. What were they? Weapons. This corresponds with the same time, according to the fossil record, that human ancestors started rapidly getting smarter, increasing their cranial capacity tremendously. What does this mean? That when we started hunting, in addition to gathering, we evolved into smarter beings. Look at the following skull sizes & shapes:

How neat is that; the addition of extra protein to our diets corresponds with the exact time period that we started evolving into smarter beings! Does this story sound familiar? And I can't help but think of that when I see this great ape trying to supplement his (mostly) fruit-based diet with some protein; good for you!

esiegel Mon, 05/12/2008 - 05:26

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So wait, are you trying to tell me that there is more evidence that the world is more than six thousand years old besides the tree you wrote about.
This might be too much for my protein enriched brain to handle.

Great blog!

One small quibble, though. The first tools weren't so much weapons used for hunting as they were scrapers and choppers used for scavenging. But hey, protein is protein, and a diet with meat means fewer calories spent digesting your food, and more calories spent thinking about how to get more food.

Orangutans Are Amazing

gregladen — Tue, 29 Apr 2008 16:39:57 +0000

Orangutans Are Amazing

This is a photograph of a male orangutan attempting to spear a fish.

It is believed that this male has seen fish spearing by local fish spearing men. This is on Kaja Island, in Borneo. Quite a few of the apes in this area are "rehabilitated" having been earlier rescued from human possession. It is often among these rehabilitated apes that we see remarkable behavior of this kind.

This method never worked out for this guy, but reports are that he later figured out how to use spearing to poach fish already caught on lines. This photo is actually published in the book Thinkers of the Jungle. The news report is here. Hat tip: Jenny Zick

gregladen Tue, 04/29/2008 - 12:39

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"reports are that he later figured out how to use spearing to poach fish already caught on lines"

So his experiences with humans have turned him into a simian delinquent? So much for "rehabilitation".

Wow, that's amazing. I bet Ben Stein couldn't do that.

The orangutan pictured is just one of hundreds living at the Nyaru Menteng Orangutan Rehabilitation Center, which is operated by the Borneo Orangutan Survival Foundation in Borneo (Indonesia) and managed by Lone Droscher Nielsen.

Kaja is a small island in the middle of the Rongan River where several dozen orangutans are living until they can be released back into a safe section of the rainforest. The problem is that due to the unchecked spreading of palm oil plantations, the forest is being cut down and orangutans are being slaughtered. This orangutan, like the 650 others at Nyaru Menteng, is an orphan. He watched as his mother was murdered and his forest home was destroyed.

You can see him and the others on the series Orangutan Island on Animal Planet.

Because of deforestation by the palm oil industry, orangutans are predicted to be extinct in the wild in less than 10 years. To learn more about orangutans and how to help them, please visit the Orangutan Outreach website at redapes.org.

Thanks, Rich

Richard Zimmerman
Director, Orangutan Outreach
http://redapes.org
Reach out and save the orangutans!

That's a very young male. Give him a little time. It takes young chimps a long time to master nut cracking. Spear fishing is trickier.

How long until they figure out how to drive? After that it's only a matter of time before they're running unlicensed taxis and kidnapping tourists.

Thank you for this.

After clicking a few links I now have my new desktop wallpaper.

http://img.dailymail.co.uk/i/pix/2008/04_05/apeMS2604_800x575.jpg

Hmmm..... We should be afraid, very afraid.

I hear this is really how the planet of the apes started.... ;)

Orangutan "Spear Fishes"

bleimanb — Tue, 29 Apr 2008 10:48:35 +0000

Orangutan "Spear Fishes"

A soon to be released book, The Thinkers Of The Jungle, by Gerd Schuster, Willie Smits and Jay Ullal, contains this first-ever image of an orangutan attempting to hunt fish with a spear. The picture was taken in Borneo on Kaja, an island where rescued apes are rehabilitated.

Only about 10 million more years of evolution and this orangutan will master the science of noodling.

bleimanb Tue, 04/29/2008 - 06:48

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I think he is qualified right now to have his own show on Fox TV.

Aren't they looking for someone still to replace the Crocodile Hunter?! This guy (or gal - I can't tell) ought to be given a chance.

I was just thinking the other day how that bear teaching itself kung fu with the stick seemed like bad news.

This has me in a blind panic.

Also, can't you see this being an Onion article? 'Tired of waiting for humans to get their shit together, orang-utans begin evolving millions of years ahead of schedule to solve the climate crisis.'

Although that's a cool photo, the splash seems to indicate that the orang is actually smacking fish with a stick more than spearing them. Which is less cool but still pretty cool.