Monkeys reason about their own thoughts, know self-doubt

Via HuffPo’s Joanna Zelman:

Apparently humans aren’t the only ones filled with self-doubt and uncertainty. A recent study found that certain monkeys question their own thinking as well.

Professor John David Smith and Michael Beran trained macaques, which are of the Old World group (native to Africa, Asia, and Europe), to play a computer game where if they got an answer right, they received a treat. A wrong answer meant no treat, but a brief pause before the next question. But there was a third option — the question mark. By selecting the question mark, the screen skipped the present question, considered too hard, and moved on to the next.

The macaques responded in the exact same way as humans — the monkeys chose to skip the tricky questions…

Meanwhile, Dr. Smith told the BBC, “Monkeys apparently appreciate when they are likely to make an error… They seem to know when they don’t know.”

Capuchins, New World monkeys (found in Central and South America), failed to choose the question mark option. Because the macaques are Old World primates, their ability to recognize their own level of thinking may reveal a step in human evolution.

The earnest side of me wants to say: This reminds me of Hume’s “Reason in Animals.”

The snarky side of me wants to say: Now that we know primates can experience self-doubt, that means they can probably be made to know existential terror:

Out of Africa–a lot earlier than expected

Via NY Times:

A cache of stone tools found on the east coast of the Arabian Peninsula has reopened the critical question of when and how modern humans escaped from their ancestral homeland in eastern Africa. The present view, based on both archaeological and genetic evidence, holds that modern humans, although they first emerged in Africa some 200,000 years ago, were hemmed in by deserts and other human species like Neanderthals and did not escape to the rest of the world until some 50,000 years ago.

An archaeological team led by Hans-Peter Uerpmann of the University of Tübingen in Germany now reports the discovery of stone tools 127,000 years old from a site called Jebel Faya in what is now the United Arab Emirates, just south of the entrance to the Persian Gulf. If the new tools were made by modern humans, as the researchers assert, then modern humans got out of Africa much earlier than believed.

The finding, reported in Thursday’s issue of Science, points to the importance of Arabia in understanding the human story. “This is a huge milestone, but unfortunately it raises more questions than it answers,” said Jeffrey Rose, an archaeologist at the University of Birmingham in England.

The major question is whether the people who reached Jebel Faya, if they were indeed modern humans, traveled farther and spread throughout the rest of the world, or whether they died out and got no farther.

The most comprehensive genetic data so far available, based on material called mitochondrial DNA, indicates that all modern humans outside Africa are descended from a single, small population that left Africa less than 60,000 years ago.

Dr. Uerpmann said that the genetic data was unreliable and that, in any case, mitochondrial DNA is a tiny fraction of the whole human genome.

Another question raised by the new finding is whether some social or cultural advance, possibly an evolutionary one, was required for modern humans to escape from Africa.

In Dr. Uerpmann’s view, the Jebel Faya tools are similar to ones found in Africa, showing that no cultural advance was required for the escape, just an improvement in climate that for a short time converted the Arabian Desert into a grassland that hunter-gatherers could cross.

This idea is at odds with a proposal advanced by Richard Klein, a paleoanthropologist at Stanford University, that the emergence of some social or behavioral advantage — like the perfection of the faculty for language — was required for modern humans to overcome the surrounding human groups. Some kind of barrier had to be surmounted, it seems, or modern humans could have walked out of Africa 200,000 years ago.

Dr. Klein said that the Uerpmann team’s case for an earlier out-of-Africa expansion was “provocative, but in the absence of human remains, it’s not compelling.”

The stone tools of this era are all much alike, and it is hard to tell whether early modern humans or Neanderthals made them. At the sites of Skhul and Qafzeh in what is now Israel, early modern humans were present around 100,000 years ago and Neanderthals at 60,000 years, but archaeologists cannot distinguish their stone tools, Dr. Klein said.

A new (which is to say very old, but recently discovered) human ancestor?

Ewen Callaway writing in Nature News:

The ice-age world is starting to look cosmopolitan. While Neanderthals held sway in Europe and modern humans were beginning to populate the globe, another ancient human relative lived in Asia, according to a genome sequence recovered from a finger bone in a cave in southern Siberia. A comparative analysis of the genome with those of modern humans suggests that a trace of this poorly understood strand of hominin lineage survives today, but only in the genes of some Papuans and Pacific islanders.

Named after the cave that yielded the 30,000–50,000-year-old bone, the Denisova nuclear genome follows publication of the same individual’s mitochondrial genome in March¹. From that sequence, Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and his colleagues could tell little, except that the individual, now known to be female, was part of a population long diverged from humans and Neanderthals.

Her approximately 3-billion-letter nuclear genome, reported in this issue of Nature², now provides a more telling glimpse into this mysterious group. It also raises previously unimagined questions about its history and relationship to Neanderthals and humans. “The whole story is incredible. It’s like a surprising Christmas present,” says Carles Lalueza Fox, a palaeogeneticist at Pompeu Fabra University in Barcelona, Spain, who was not involved in the research.

When the ancient genome was compared to a spectrum of modern human populations, a striking relationship emerged. Unlike most groups, Melanesians — inhabitants of Papua New Guinea and islands northeast of Australia — seem to have inherited as much as one-twentieth of their DNA from Denisovan roots. This suggests that after the ancestors of today’s Papuans split from other human populations and migrated east, they interbred with Denisovans, but precisely when, where and to what extent is unclear.

More answers could come from a closer look at Denisovan, human and even Neanderthal DNA. So far, conclusions about interbreeding have been drawn from a relatively small number of human genomes using conservative DNA-analysis methods, says David Reich, a geneticist at Harvard Medical School in Boston, Massachusetts, who led the Denisova analysis. “There may have been many more interactions,” he says. Pääbo says it may be possible to determine roughly when humans interbred with Denisovans by examining the length of DNA segments lurking in various human genomes, with shorter segments corresponding to more shuffling of genes and a longer elapsed time.

A molar discovered in the same cave also yielded mitochondrial DNA resembling that of the finger bone. But the Denisovans were probably more widespread, says Pääbo. Some fossils from China, for example, resemble neither Neanderthals nor modern humans — nor Homo erectus, an earlier human ancestor. Pääbo wonders whether they could be more closely related to Denisovans. His Russian collaborators plan to search for more complete Denisovan fossils that could be matched to others from China.

Chris Stringer, a palaeoanthropologist at London’s Natural History Museum, agrees that Asian fossils, such as the 200,000-year-old Dali skull from central China, could have links to the Denisovans. But he says that firm conclusions about such relationships will have to await the discovery of more complete Denisovan fossils.

Preserved DNA from other Asian fossils would also provide a clearer picture of the Denisovans, which Pääbo, to sidestep controversy, has opted not to call a new species or subspecies of hominin. The challenge will be to make sense of such discoveries and put them in the context of ancient human history, says Lalueza Fox. Palaeoanthropologists are just beginning to scrutinize the Neanderthal genome published earlier this year³ for clues to ancient human history. With the Denisova genome, “they will need to deal with another surprise”, he says.

Is the As-bacterium overhyped?

Obnoxious-even-when-he’s-right atheist and University of Minnesota Morris biologist PZ Myers says “yes.”  The Weiner sequence, it appears, has played out again.

My own speculation that the bacterium might represent the trunk of a new evolutionary tree does now seem, as I expected, reckless.

The piece is long, but non-technical, so bear with us.

Here’s the story. Life on earth uses six elements heavily in its chemistry: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur, also known as CHNOPS . There are other elements used in small amounts for specialized functions, too: zinc, for instance, is incorporated as a catalyst in certain enzymes. We also use significant quantities of some ions, specifically of sodium, potassium, calcium, and chloride, for osmotic balance and they also play a role in nervous system function and regulation; calcium, obviously, is heavily used in making the matrix of our skeletons. But for the most part, biochemistry is all about CHNOPS.

Here’s part of the periodic table just to remind you of where these atoms are. You should recall from freshman chemistry that the table isn’t just an arbitrary arrangement — it actually is ordered by the properties of the elements, and, for instance, atoms in a column exhibit similar properties. There’s CHNOPS, and notice, just below phosphorous, there’s another atom, arsenic. You’d predict just from looking at the table that arsenic ought to have some chemical similarities to phosphorus, and you’d be right. Arsenic can substitute for phosphorus in many chemical reactions.

This is, in fact, one of the reasons arsenic is toxic. It’s similar, but not identical, to phosphorus, and can take its place in chemical reactions fundamental to life, for instance in the glycolytic pathway of basic metabolism. That it’s not identical, though, means that it actually gums up the process and brings it to a halt, blocking respiration and killing the cell by starving it of ATP.

Got it? Arsenic already participates in earthly chemistry, badly. It’s just off enough from phosphorus to bollix up the biology, so it’s generally bad for us to have it around.

What did the NASA paper do? Scientists started out the project with extremophile bacteria from Mono Lake in California. This is not a pleasant place for most living creatures: it’s an alkali lake with a pH of close to 10, and it also has high concentrations of arsenic (high being about 200 µM) dissolved in it. The bacteria living there were already adapted to tolerate the presence of arsenic, and the mechanism of that would be really interesting to know…but this work didn’t address that.

Next, what they did was culture the bacteria in the lab, and artificially jacked up the arsenic concentration, replacing all the phosphate (PO₄^3-) with arsenate (AsO₄^3-). The cells weren’t happy, growing at a much slower rate on arsenate than phosphate, but they still lived and they still grew. These are tough critters.

They also look different in these conditions. Below, the bacteria in (C) were grown on arsenate with no phosphate, while those in (D) grew on phosphate with no arsenate. The arsenate bacteria are bigger, but thin sections through them reveal that they are actually bloated with large vacuoles. What are they doing building up these fluid-filled spaces inside them? We don’t know, but it may be because some arsenate-containing molecules are less stable in water than their phosphate analogs, so they’re coping by generating internal partitions that exclude water.

What they also found, and this is the cool part, is that they incorporated the arsenate into familiar compounds^*. DNA has a backbone of sugars linked together by phosphate bonds, for instance; in these baceria, some of those phosphates were replaced by arsenate. Some amino acids, serine, tyrosine, and threonine, can be modified by phosphates, and arsenate was substituted there, too. What this tells us is that the machinery of these cells is tolerant enough of the differences between phosphate and arsenate that it can keep on working to some degree no matter which one is present.

So what does it all mean? It means that researchers have found that some earthly bacteria that live in literally poisonous environments are adapted to find the presence of arsenic dramatically less lethal, and that they can even incorporate arsenic into their routine, familiar chemistry.

It doesn’t say a lot about evolutionary history, I’m afraid. These are derived forms of bacteria that are adapting to artificially stringent environmental conditions, and they were found in a geologically young lake — so no, this is not the bacterium primeval. This lake also happens to be on Earth, not Saturn, although maybe being in California gives them extra weirdness points, so I don’t know that it can even say much about extraterrestrial life. It does say that life can survive in a surprisingly broad range of conditions, but we already knew that.

So it’s nice work, a small piece of the story of life, but not quite the earthshaking news the bookmakers were predicting.

Newly discovered bacteria redefines possibilities of biochemistry

What can life be made of? Stanislaw Lem imagined beings made of ice, of uranium, and of precious gems. Now, NASA scientists have discovered organisms made of arsenic. Via Gizmodo’s Jesus Diaz:

NASA scientist Felisa Wolfe Simon will announce that they have found a bacteria whose DNA is completely alien to what we know today. Instead of using phosphorus, the bacteria uses arsenic. All life on Earth is made of six components: carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur. Every being, from the smallest amoeba to the largest whale, share the same life stream. Our DNA blocks are all the same.But not this one. This one is completely different. Discovered in the poisonous Mono Lake, California, this bacteria is made of arsenic, something that was thought to be completely impossible. While she and other scientists theorized that this could be possible, this is the first discovery. The implications of this discovery are enormous to our understanding of life itself and the possibility of finding beings in other planets that don’t have to be like planet Earth.

No details have been disclosed about the origin or nature of this new life form. We will know more today at 2pm EST but, while this life hasn’t been found in another planet, this discovery does indeed change everything we know about biology.

Now, I have no scientific training–seriously, none at all, I majored in journalism and English–and I’m speculating wildly here from a position of near total ignorance of the biochemistry and eukaryote evolution; but given that that the Mono Lake bacteria has DNA funamentally different from any other observed organism, this could mean that life arose independently more than once on Earth.

Reverse-engineering beauty

Denis Dutton theorizes on the Pleistocene origin of our aesthetic sense at TED; illustrations by Andrew Park:

 

 Here is a brief interview Dutton conducted with Jorge Louis Borges, unrelated to anything discussed in the lecture. Why link it, then? Because of rational beings, one sort is divine, one is human, and another is such as Borges.