On why Darwinism fails as search strategy.

ntelligent Design in Action: Optimization

Evolution News & Views September 16, 2015 3:59 AM

In the past we've discussed several sciences that rely on principles of intelligent design: among them, archaeology, forensics, cryptology,informatics, SETI and SEETI, and more. Now a paper describing a remarkable achievement offers the opportunity to explore another: optimization. The paper by University of Washington machine-learning researchers Abram Friesen and Pedro Domingos is well described in aUW news item. Jennifer Langston defines optimization and tells how useful the field is.

The key to solving many of the most important problems in business, science and technology lies in optimization --finding the values for variables that give you the highest benefit.

Whether those are which stocks to buy, which search results to return, what best predicts the outcome of the next presidential election or which amino acids to string together in a new drug to fight malaria or cancer, optimization is crucial to getting what we want. When a problem is simple, we can program a computer to solve it. When it's too complex for that, optimization is how the computer finds the solution by itself. [Emphasis added.]

We all know a computer is incapable of finding a solution all by itself. An appropriate algorithm designed into it, however, can seemingly hit the jackpot automatically.

In essence, optimization is a search strategy. William Dembski deals extensively with search in his latest book, Being as Communion. Search is closely tied to the concept of information, which Dembski defines as a winnowing process that realizes possibilities by ruling out others. If the information desired is a solution with the highest benefit, a search must be conducted for that information. The science of optimization, therefore, is the study of algorithms or strategies that realizes the optimum solution by ruling out others. As such, it is an information-rich field.

Friesen and Domingos have scored an impressive achievement in this field. Their new optimization algorithm, named RDIS, performed an optimization task between 100,000 and 10 billion times more accurately, on average, than standard techniques. It was so good it won the top prize at the 24^th International Joint Conference on Artificial Intelligence in July. This giant leap in optimization can help speed up finding solutions listed by Langston, and others like road recognition for self-driving cars and determining folds for custom proteins.

Domingos explains why optimization is more important than many people realize:

"In some ways optimization is the most important problem you've never heard of because it turns up in all areas of science, engineering and business. But a lot of optimization problems are extremely difficult to solve because they have ahuge number of variables that interact in intricate ways," said senior author Pedro Domingos, UW professor of computer science and engineering.

Figuring out protein folds, for instance, has been a long-standing problem. A protein begins with a chain of amino acids, but folds into a complex, three-dimensional shape. For all but small proteins, predicting the shape from the chain -- given that the amino acids interact in complex ways -- has defied many previous searches. RDIS may be able to speed the solution for synthetic drugs by optimizing the amino acid sequence for the desired shape. Another application is to determine a three-dimensional shape from a series of two-dimensional images.

Making RDIS work so well relied on several techniques. One was a divide-and-conquer strategy called decomposition. By breaking down the problem into smaller problems and treating them as independent problems (even though they are not), the designers converged on the optimal solution much faster. Another strategy is recursion. These and other technical details are described in the paper.

Optimization is not limited to AI or computers. Every logically thinking person faces optimization problems; e.g., "How shall I distribute my funds to optimize my return on investment?" "What players shall I call up for this football play?" "Shall I drop off the kids at school before going to the bank, or after?" "Where is traffic likely to be worse?" Optimization rapidly becomes more difficult as the complexity of the problem rises, indicated in a pithy analogy:

Solving optimization problems is like being left blindfolded at the top of a hill and asked to walk to the ocean. One way to do that is to judge where to go by feeling around with your foot and taking one step a time in the steepest downward direction. That works if there's only one hill. But if you're at the top of the Himalayas, you'll quickly get stuck because there are thousands of peaks and foothills and flat parts. That's essentially what happens with current optimization algorithms.

"If you're lucky, maybe you'll wind up in the sea but more likely you'll wind up in a valley or a lake," said Domingos. "If you could see the whole landscape, you'd say 'oh, here's where I have to go,' but the problem is you can't see everywhere and neither can today's algorithms."

This analogy will sound familiar to those acquainted with evolutionary biology. The "fitness landscape" metaphor coined by Sewall Wright deals with hills and valleys, too; in that context, peaks represent high fitness and valleys represent low fitness. Wright and subsequent evolutionary theorists realized that organisms could get stuck on local fitness peaks (optima). Reaching a higher fitness peak would require losing fitness temporarily to cross a valley (see "Complexity by Subtraction"). And yet it appears frequently that animals did cross valleys, losing and regaining traits multiple times according to phylogenetic trees. Could organisms reach high levels of fitness by blind, unguided processes?

It's obvious that Friesen and Domingos did not design RDIS to rely on blind search. It was intelligently designed, in multiple ways, throughout. First, they had to know a lot about existing optimization tools. Second, they had to understand their goal. Third, they had to design multiple interacting factors to achieve their goal. It's also a case of hierarchical design. In a real sense, they had to optimize their optimization tool.

Intelligent designers know how to cross valleys to reach higher peaks, because they can see a distant goal and aim for it. Natural selection has no foresight. Portraying neo-Darwinism's mechanisms as optimization strategies is, therefore, wishful thinking (see "Evolutionary Computing: The Invisible Hand of Intelligence"). Dembski has shown in Being as Communion and in his earlier book No Free Lunch that no search strategy is superior to blind search -- unless information is added to the system by intelligence.

Optimization is a good example of intelligent design at work in the sciences. Not only is the field permeated with ID concepts from start to finish, it is also highly useful and widely applicable. So is ID a "science stopper" as Darwinists often claim? Quite to the contrary.

Lamarck's revenge II

Natural Genetic Engineering? Natural Popcorn? Or Something More Important?

Denyse O'Leary September 15, 2015 3:47 AM 

It is just not Darwin's world any more. Life forms share genes,irrespective of ancestry, pick up traits during their lifetimes that they pass on, can lose key functions and then get them back later, and treat their genomes like projects under construction.

It is certainly not the world anyone expected to find when we first started mapping genomes. The scientist best known for pulling together some ideas around natural genetic engineeringis bacterial geneticist James Shapiro, author ofEvolution: A View from the 21st Century (2011).

He also wrote a series of essays at theHuffington Post, noting, as sympathetic book reviewer Franklin Harold (Department of Microbiology, University of Washington) puts it:

Briefly, the architecture of genomes turned out quite unlike what had been expected. In higher organisms, at least, genes are composed of both coding and non-coding sequences, and must be spliced prior to expression. Classical protein- coding sequences make up an astonishingly small proportion of the genome, just a few percent. The remainder features regions that specify an intricate network of regulatory elements, many based on RNA rather than proteins. These are concerned, not only with the expression of individual genes, but with the fidelity and architecture of the genome as a whole. Genomes also contain numerous stretches, long and short, of repetitious DNA, whose physiological functions are not obvious.

...

At first sight, the continuous makeover seems merely to supply more variations for selection to winnow, but Shapiro argues that there is much more to it than that. Natural genetic engineering generates different kinds of variation from those produced by classical mutations, one gene at a time. Rearrangements can take place at multiple locations at once and shuffle entire domains from one protein to another, producing novel combinations quickly and abruptly, perhaps even purposefully. Genomes, it seems, are built to evolve -- not at the petty pace of classical genetics, but in leaps that entail rearrangement of the genetic architecture or the import of foreign information. So could this be the way that organisms generate the multiple, coherent variations that seem required to manufacture complex organelles such as eyes or flagella? At the end of the day, that is a question that must be answered by experiment; we are not there yet, but the technology to address such issues is coming to hand.

That said, he argues that we can deal with all these questions without really major conceptual changes (2013):

If experiments show that cells can make distinct appropriate NGE responses to different adaptive challenges occurs, we need to figure out how they do so. This almost certainly would prove to be more than a strictly mechanical process. How do cells carry out their computations to make useful goal-oriented responses? A successful answer to that question will certainly involve cybernetics. If such investigations take evolution science into areas that are more than strictly material, so be it. As long as we stay within the realm of natural processes, there are no boundaries on what science can address.

But some of us are not so sure. Philosopher James Barham thinks the main issue is seeing life forms as if they were machines:

We are finally beginning to realize, on the basis of irrefutable empirical evidence, as well as more careful analysis of Darwinian theory itself, that purposeful action in living things is an objectively real phenomenon that is presupposed, not explained, by the theory of natural selection.

Yes, that is the problem: Why does the animal want to live?

We can build machines -- we create them to do what we want -- and then put them out with the trash. But not free-living life forms. They try to survive. To deny this would require us to say, as Barham notes, that purpose is an illusion.

Part of the problem between Barham and Shapiro, which led to an exchange of views, sounds conceptual. What does Dr. Shapiro mean by "natural" processes, as opposed to "more than strictly material" ones, as above? A strictly material process would be a series of events fully explained by material processes (for example, what happens when a loose stone falls off a cliff).

But some entities in nature are not material at all: the number 7 comes to mind. Some philosophers have argued that we can construct a theory of items grouped by sevens without using a concept like 7. But whatever advantages these philosophers' suggestion may offer, it does not represent what people do. We have an immaterial concept of 7 that organizes items and events, instantiated in various media at various times. It is natural without being material in any meaningful way.

Life forms seem to be somehow in between. They are material, but unlike stones, they don't just exist. They want to exist, and to go on existing. They often seem to have a number of additional, related goals.

If Dr. Shapiro can account for the purposeful way in which life forms strive to sustain their own existence as part of a natural world, it is -- as he clearly recognizes -- a natural world that is far removed from the Darwinism of the science textbooks, which emphasizes the random nature of these processes.

Well, we must shortly look at the Darwinism of the textbooks.

Matter over mind?

Group Delusions Aside, Sentient Robots Aren't on the Way

Erik J. Larson March 26, 2015 11:33 AM 

Our colleague Wesley Smith commented yesterday on a piece in Nature,ntelligent robots must uphold human rights." We read there:

There is a strong possibility that in the not-too-distant future, artificial intelligences (AIs), perhaps in the form of robots, will become capable of sentient thought. Whatever form it takes, this dawning of machine consciousness is likely to have a substantial impact on human society.

More:

Academic and fictional analyses of AIs tend to focus on human -- robot interactions, asking questions such as: would robots make our lives easier? Would they be dangerous? And could they ever pose a threat to humankind?

These questions ignore one crucial point. We must consider interactions between intelligent robots themselves and the effect that thesee exchanges may have on their human creators. For example, if we were to allow sentient machines to commit injustices on one another -- even if these 'crimes' did not have a direct impact on human welfare -- this might reflect poorly on our own humanity. Such philosophical deliberations have paved the way for the concept of 'machine rights'.

"Machine rights"? I have to confess, when I read articles like this I have an almost visceral reaction. It amounts to a full-blown, ongoing perplexity and fascination with the capacity of otherwise intelligent people to engage in serious-sounding group delusion. To pick this apart is a little like explaining to someone why his interest horoscopes is probably untethered to any genuine scientific knowledge about the planets, the relevant laws governing their motion, and so on. I'm tempted to say, "Yes, that's right, the robots are becoming intelligent so quickly that they may soon take control. In fact, here they come now! Run for cover!"

Let's do some not-too-painful sanity checking. What is the current state of robot technology? MIT is famous for cutting-edge work on robots (cf. Rodney Brooks), and they've got a robot that is getting better at identifying large objects like plates, as distinct from, say, a salad bowl.

Meanwhile in manufacturing, the latest three-hundred-pound gadget designed to grab and manipulate plastic components (I gather) is getting so smart than when a component topples over, it can move it's claw over to pick it up.

The serious point here is that the current state of robotics tells a different tale from robots "coming alive" in the near future and taking control of human society. The technical challenges to simulating actual human intelligence are vast and daunting. If fluff articles from no less than Nature must continue to bombard hapless readers with sci-fi fantasies about the coming intelligence revolution, I suggest they should first offer the simplest form of evidence apart from sheer rhetorical emotivism.

For example, let's have a URL to an article describing an actual robotic system, leveling with the reader on the actual capabilities of the system. I offer bonus points for explaining how apparently simple problems like moving around in a dynamic environment -- a street corner! -- confounds current systems. I offer even more bonus points for explaining why the supposedly smart robot can't understand your easy conversational banter with it -- at all.

AI systems (robots' brains) and full robotic systems suffer from two limitations that show no signs of going away, now or in any foreseeable future. First, there is the inability to keep track of aspects of their environment that become relevant as a function of time -- dynamic environments, where things change as the robot moves through it, in other words, the real world. Second, there is the inability to keep track of aspects of language that keep changing as a function of time -- conversation, in plain and simple everyday terms.

The Turing Test has been debated since the inception of AI in the 1950s, and to date it shows no sign of yielding to gargantuan increases in hardware performance via Moore's Law, or advances in algorithmic techniques, such as convolutional neural networks, or so-called Deep Learning. An enthusiast with the stripes of, say, Ray Kurzweil overwhelms the uninformed with scientific-looking graphs showing exponential progress toward superintelligence. Yet a simple graph of improvements on the Turing Test over the years would be decidedly flat, and downright embarrassing.

I wonder what Bill Gates or Elon Musk or any other luminary enthralled with the current rhetoric about a coming AI would say to such a graph? The smart money is on looking at the problem without sci-fi goggles, separating it from other, narrower problems where human intelligence is decomposable into a set of representations and algorithms that admit of automation, and clarifying the actual landscape so that other, serious scientists and interested parties can productively discuss the roles of computation and human thinking in society.

It's a myth that the dividing line between man and machine is essentially temporary, and that all problems once thought solely in the purview of human intelligence will eventually yield computational solutions. We're going backward with the Turing Test, for instance, as the latest Loebner Prize competition demonstrated: Eugene Goostman simulates a vapid, sardonic 13-year-old Ukrainian speaking broken English to fool a few people for a few minutes (who no doubt are performing backbends to reduce their own standards of conversation with actual persons, in hopes of a history-making moment with a mindless chatterbot).

There's no real response to what I've just said. I mean, no one seriously thinks computers are making substantial let alone exponential progress on actual natural language interpretation or generation in non-constrained domains -- yet by sleight of hand, ignorance, overenthusiasm, blurry vision, dyspepsia, or what have you, provision of seemingly related examples (chess, driverless cars, Google Now for recommendations, or Siri for voice recognition, perhaps) keeps the parlor tricks alive, and claims of inexorable progress continue.

There is progress on computation, of course, but it has little to do with the machines themselves acquiring actual intelligence. It has everything to do with researchers in computer science and related fields continuing to use their own creative intellects to find clever ways to represent certain tasks that admit of algorithmic decomposition, such that the tasks can be mapped onto digital computer hardware. Our intelligence itself does not appear to be so reducible.

And so these discussions are a tempest in a teapot. Who's really preparing for the robot future? And here let's avoid equivocating between an economy increasingly dominated by dumb automation, and a world inhabited by truly intelligent digital beings. Who's worried about the latter? I mean, beyond relatively uninformed, self-styled futurists (that most coveted of social roles), or nose-against-the-glass software junkies in the Valley, binge-watching digitally-remastered editions of Blade Runner, and speculating about "dating their operating systems," as director Spike Jones offered up, memorably, complete with the sultry voice of Scarlett Johansson in his 2013 hit movie Her.

Sci-fi fantasies dressed up as serious "What if?" discussions are not new, of course. Wormholes have a basis in actual science (but probably are still not possible). I'd rather see a perpetual shouting match about the coming of time travel, like back in the Star Trek days. It'd be sci-fi still, but actually closer to reality than the imminent-smart-robots palaver today. There's a discussion to be had about computation in society, certainly, but it's not the silly one we are having.

File under 'well said' VII

Frederick Douglas"It is easier to build strong children than to repair broken men"

Climate change?:Been there,done that.

By Colin Barras

14 September 2015

In the late 1980s, as the world's governments were waking up to the problem of climate change, the mud at the bottom of the ocean near Antarctica revealed a surprise. Earth had lived through rapid global warming before.
About 55 million years ago global temperatures spiked. Then, as now, sea levels rose, the oceans became more acidic, and species disappeared forever.
Little wonder, then, that researchers view this ancient event – known as the "Palaeocene-Eocene Thermal Maximum" or PETM – as a potential goldmine of useful information for understanding modern climate change.
We now know that the PETM was one of the most rapid and dramatic instances of climate change in Earth's history. Its causes are still up for debate, but there seem to be eerie parallels with the causes of modern climate change. What is absolutely clear is that the PETM's effects were far-reaching. It may have altered the course of life on Earth.
 published their findings in 1991. They reported that the shells of tiny planktonic fossils in the muds had betrayed the rapid temperature swings.
The PETM seems to have been caused by greenhouse gases just like modern-day climate change
More precisely, it was the oxygen isotopes locked away in those shells. At around the 55-million-year mark, the amount of "heavy" oxygen-18 in the shells rose relative to "lighter" oxygen-16.
That greater abundance of oxygen-18 is a sure sign that conditions were getting warmer. Water evaporates more readily at higher temperatures, and it's the "light" oxygen-16 that is most easily vapourised. This means that warmer water contains more oxygen-18, and the plankton living in warmer water incorporate more of the stuff into their shells.

Those planktonic shells turned out to be useful for another reason. They hinted at exactly why ocean temperatures rose.
This is because of the carbon they contain.
Today's global warming is not simply a rerun of the PETM
Like oxygen, carbon exists in different isotopic forms. At exactly the same time that the plankton shells became rich in oxygen-18, they also began carrying much more carbon-12 relative to carbon-13. The oceans must suddenly have gained a big supply of carbon-12.
This is something that generally happens after a massive injection of carbon-rich greenhouse gases – carbon dioxide (CO2) or methane – into the atmosphere.
In other words, the PETM seems to have been caused by greenhouse gases just like modern-day climate change.

But today's global warming is not simply a rerun of the PETM. Earth was a very different place 55 million years ago.
One of the biggest concerns today is that the Antarctic ice sheet is shrinking because of climate change. This wasn't a problem during the PETM, because there probably was no Antarctic ice sheet. Even before the onset of the PETM, global temperatures were several degrees warmer than they are now.
All researchers agree that the unusually warm conditions lasted about 170,000 years
Some researchers think the pace of climate change during the PETM distinguishes the event from today too. A controversial study published in 2013 made the case.
Researchers examined another set of muds that formed at the bottom of the ocean 55 million years ago, this time in the north-west Atlantic. They found banding in the muds that they argued was formed by annual cycles.

When they traced the oxygen and carbon isotope blips associated with the PETM, they found that they were contained in just 13 bands. This means, they said, that the PETM temperature surge came in just 13 years.

This does not imply that the PETM came and went in little more than a decade. All researchers agree that the unusually warm conditions, with global temperatures at least 5 °C above average, lasted about 170,000 years.

Modern climate change doesn't have such a dramatic trigger

What it would imply is that global temperatures ramped up to that 5 °C figure in just 13 years. Today, in contrast, global temperatures have risen about 1 °C since the late 19th century.

If PETM climate change really were so rapid, there would be implications for the event that triggered the warming. To create such a rapid rise in global temperature, the atmosphere would have had to be flooded with greenhouse gases almost literally overnight.

Perhaps the release of gases from the melting of a huge carbon-rich comet that flew too close to the Earth would do the trick. Modern climate change doesn't have such a dramatic trigger.

But it's important to stress that many researchers strongly reject that 13-year figure.

There are all sorts of problems with the idea, says Richard Zeebe at the University of Hawaii at Manoa. Most importantly, it is physically impossible for the oceans to heat up that quickly.

Most researchers think the PETM warming really took place over a long period

The Earth's oceans contain a vast amount of water, and heating it up takes time. Even if there was a massive and sudden injection of CO2 into Earth's atmosphere, the oceans simply could not heat up in just 13 years.

"You can heat up the atmosphere relatively quickly, but it takes centuries to millennia to heat up the oceans," says Zeebe.

Other researchers now suggest that the 13 bands in the rock must each represent centuries, not single years. That's if the bands are real at all: some sediment drilling experts say they might simply be an artefact of the drilling process the researchers used to extract the muds.

Most researchers think the PETM warming really took place over a  long period, but exactly how long is still up for discussion.

 One 2011 estimate suggests that the carbon was released over a period of perhaps 20,000 years.

Such a slow release is very different from today. It might indicate that the greenhouse gases came from the relatively gradual release of gases from volcanic activity.

It looks like the carbon was released into the atmosphere over about 1500 years

Research published in 2014 points to a middle ground. Gabriel Bowen at the University of Utah in Salt Lake City and his colleagues examined the carbon isotopes preserved in soils that formed 55 million years ago in what is now Wyoming.

Whereas the ocean sediments tell us about conditions in the PETM oceans, the soils sample the PETM atmosphere, which responds more rapidly to climate change.

The by-now-familiar surge in carbon-12 popped up again, this time preserved in carbonate nodules that grew in the soil. In this case, it looks like the carbon was released into the atmosphere over about 1500 years: a timescale that looks more similar to today's atmospheric changes.

The ancient soils also indicate the pace of carbon emissions

 The researchers calculated that something approaching 1 billion tonnes of carbon entered the ancient atmosphere each year. That is within an order of magnitude of the current annual release rate of 9.5 billion tonnes.

In light of these findings, the PETM looks like a more reasonable model for today's climate change.

When the oceans warm up a little, vast deposits of methane that are "frozen" in the seabed begin to melt

Bowen and his colleagues made another discovery in Wyoming. They realised that there were actually two distinct pulses of warming 55 million years ago.

A few thousand years before the PETM itself, a vast quantity of carbon-rich greenhouse gases entered the atmosphere from an unidentified source, again at a rate of about 1 billion tonnes per year.

The environment seemed seems to have almost brushed off this "pre-onset event". Atmospheric temperatures rose, but within a couple of thousand years they fell again. Conditions had apparently returned to normal.

The fall in atmospheric temperatures probably came about because the oceans absorbed the heat from the pre-onset event. That might have paved the way for the PETM itself.

 When the oceans warm up a little, vast deposits of methane that are "frozen" in the seabed begin to melt. The methane – a potent greenhouse gas – bubbles up, enters the atmosphere and raises global temperatures.

I think that in general the jury is still out

This leads to more ocean warming, triggers more methane release from the seabed, and causes atmospheric temperatures to rise more, and so on. Soon the planet becomes very warm, which is exactly what happened 55 million years ago during the PETM.

Something similar might be happening today. As the modern oceans warm there is good evidence that methane is once again bubbling up from the seabed. The PETM offers us a preview of where that can lead.

However, all of these explanations for the onset of the PETM are still just proposals. There is no scientific consensus on the exact cause of the PETM, beyond the fact that it clearly involved a release of greenhouse gases from somewhere.

"I think that in general the jury is still out," says Bowen.

While the PETM's exact cause is still elusive, its effects are clear

Under the more controversial scenarios, like the idea of a passing comet, the trigger for the event and the pace of climate change have very few parallels with the warming our planet is now experiencing.

Under the more plausible scenarios, like the snowballing release of methane from beneath the sea, the parallels with today are clear.

Regardless, while the PETM's exact cause is still elusive, its effects are clear.

 Even back in 1991 when it was first described, it was evident that the PETM was a killer.

Other microbes may have taken advantage of those oxygen-poor conditions

Some of the microfossil species preserved in the Antarctic sediments disappeared as the warming began. The species impacted were those that lived deep in the oceans. They experienced their most severe extinction in tens of millions of years.

Curiously, many microscopic species that lived in the shallower ocean waters actually flourished – an early sign that there were winners and losers as the climate changed.

It was probably a combination of factors that killed the deep-sea species. The warmer temperatures would have been unwelcome, but there may also have been less oxygen available in that warmer water.

However, other microbes may have taken advantage of those oxygen-poor conditions.Some oceanic sediments from the time contain high quantities of an iron-rich magnetic mineral called magnetite. Some species use magnetite in their bodies: either because of its hardness (it makes good teeth) or its magnetic properties (it can allow some species to orientate themselves with the Earth's magnetic field).

The world's coral reefs faced one of their five greatest crises since they first evolved

Iron can build up in poorly-oxygenated water, so the conditions in the PETM oceans might have led to a radiation of microscopic species using magnetite.

Seawater changed in other ways that were clearly harmful. When the oceans absorb greenhouse gases like carbon dioxide, the process produces a mild acid in the water, lowering the pH: a phenomenon known as ocean acidification. We know it is happening in the world's oceans today, and it happened 55 million years ago too.

Then, as now, ocean acidification was bad news for marine species that build skeletons out of calcium carbonate, because this solid mineral begins to dissolve when the pH drops. Acidification might have been a factor in the deep-sea extinction, and it also affected some shallow living species.

In particular, the world's coral reefs faced one of their five greatest crises since they first evolved 550 million years ago.

There were changes on land too.In the Arctic, plenty more rain than usual fell during the PETM, probably because stronger ocean evaporation in the tropics delivered more water vapour to higher latitudes.

Seas might have risen by as much as 30m

Geologists have also found evidence, from the styles of rock that formed 55 million years ago, that dry coastal environments were deluged by rising sea levels.

There was little ice to melt, so the sea level rise was probably modest: perhaps in the region of 5m, caused by the expansion of water as it becomes warmer. However, in a worst-case scenario the sea level rise could have been more severe.

For instance, there was magmatic activity in the north Atlantic at roughly this time. That might have warmed up the ocean crust and pushed it upwards, making the oceans shallower than usual and accentuating any sea level rise. Consider factors like this and seas might have risen by as much as 30m.

For life on land, the warm PETM conditions led to dramatic changes.In Wyoming, plant ranges shifted hundreds of kilometres north as temperatures rose. Conifers apparently disappeared from the area entirely, only returning as temperatures fell after the PETM.

There is strong evidence that about 40% of the mammalian fauna got smaller during the PETM

Some plant species disappeared from the tropics too, but there is evidence that plant diversity actually rose overall here. That may have been a consequence of both the warmer conditions and higher levels of the carbon dioxide plants use to make their food.

The PETM also marks the moment when many of the mammal groups that dominate the world today – including horses, cattle and other hoofed animals – appeared and spread across the northern continents. They probably did so probably in response to the warmer conditions.

But members of these familiar animal groups would have looked odd to our eyes.

"There is strong evidence that about 40% of the mammalian fauna got smaller during the PETM," says Ross Secord at the University of Nebraska in Lincoln. "Nothing appears to have gotten larger."

Some mammals became very small indeed.In 2012, Secord and his colleagues looked at fossils of Sifrhippus sandrae, a species of early horse that lived in what is now Wyoming.

At the onset of the PETM, when horses first appeared in the fossil record, Sifrhippus was diminutive: it weighed about 5.6kg.

As the temperatures rose, Sifrhippus became even smaller. 130,000 years into the PETM, some adults probably tipped the scales at about 3.9kg: a modest weight for a domestic cat.

At the end of the PETM, as temperatures dropped, Sifrhippus grew again.

Other mammalian herbivores shrank too, and so did some mammalian carnivores.These size changes might be down to something called Bergmann's rule, says Secord. This says that warm-blooded animals tend to be relatively small in warm regions and larger in cold ones.

When atmospheric CO2 levels rise, the leaves and shoots of plants may become less nutritious

That could be because, in cold regions, it is useful to have a larger body – and a smaller relative surface area – to prevent losing too much body heat.

But Bergmann's rule is usually used to explain why animals in the tropics are smaller than those at higher latitudes, not to explain why animals grew to different sizes as a response to global warming.

Other researchers have suggested other reasons for the PETM changes in mammal size.

In 2013, Philip Gingerich at the University of Michigan in Ann Arbor suggested the mammals might have been responding to changes in vegetation brought on by the PETM.

We have learned a lot about the PETM in the quarter-century since its discovery

When atmospheric CO2 levels rise, the leaves and shoots of plants may become less nutritious and harder for herbivores to digest. If that happened during the PETM, it could have led to slower animal growth, and herbivores might have begun to shrink. Carnivores, forced to target smaller prey, might have followed suit.

Peter Stiling at the University of South Florida in Tampa has investigated this. In 2007 he found that, in a high-CO2 atmosphere, oak leaves did carry less nitrogen. "As a result, herbivores often eat more to compensate," he says.

But there's no direct evidence as yet that herbivores, or the carnivores that eat them, grow more slowly and become smaller adults as a consequence.We have learned a lot about the PETM in the quarter-century since its discovery, but clearly there are plenty of questions left to answer.

Our particular branch of the primate tree had flourished to such a degree that the world really had become the planet of the apes

One of the most intriguing is whether the warming 55 million years ago was instrumental in the evolution of the first true primates: the group that ultimately gave rise to our species.

Modern primates appeared and spread at the beginning of the PETM, alongside horses and other hoofed animals. Their early fossil record is patchy, but they appear at almost exactly the same time in Asia, Europe, the Americas and Africa.

Within a few tens of millions of years, our particular branch of the primate tree had flourished to such a degree that the world really had become the planet of the apes. About 5 million years later, the first upright apes we recognise as our direct ancestors appeared.

Would primates have become so successful if the PETM had never happened? No one can say for sure.

Paved with the best intentions.

The Human Side of Trophy Hunting:
Wesley J. Smith September 14, 2015 9:00 AM


I am no fan of trophy hunting. But the recent hysteria that has seen bans instituted in a few African countries is causing real harm to humans.

That is the gist of the (surprising) New York Times story about how a hunting ban in Botswana has hurt villagers in their pocketbooks and threatened their safety. From the story:

Since Botswana banned trophy hunting two years ago, remote communities like Sankuyo have been at the mercy of growing numbers of wild animals that are hurting livelihoods and driving terrified villagers into their homes at dusk.
The hunting ban has also meant a precipitous drop in income. Over the years, villagers had used money from trophy hunters, mostly Americans, to install toilets and water pipes, build houses for the poorest, and give scholarships to the young and pensions to the old.

These bans are causing material harm to the villagers. It isn't as if the villagers aren't killing the animals in self-defense. In addition, when hunting is allowed, the locals engage in better conservation practices because it is in their economic interest:

Where trophy hunting benefits communities, locals are more motivated to protect wild animals as a source of revenue, experts say. But in most places without trophy hunting, they are simply considered a nuisance or danger, and locals are more likely to hunt them for food or to kill them to defend their homes and crops.
The locals want a return to the hunt.

But in Sankuyo and other rural communities living near the wild animals, many are calling for a return to hunting. African governments have also condemned, some with increasing anger, Western moves to ban trophy hunting. "Before, when there was hunting, we wanted to protect those animals because we knew we earned something out of them," said Jimmy Baitsholedi Ntema, a villager in his 60s. "Now we don't benefit at all from the animals. The elephants and buffaloes leave after destroying our plowing fields during the day. Then, at night, the lions come into our kraals."
Who cares about them? Animal rights Western activists don't, and they easily pressure our increasingly politically correct corporations into knee-jerk reactions --such as Delta, which recently banned shipping hunting trophies on its flights -- without a full knowledge of pertinent facts.

This is precisely why an "animal rights" approach to animal husbandry and welfare issues -- that focuses exclusively on the animals while ignoring the human element -- is so short-sighted.


The right way to go is animal welfare, which takes into account the human benefit as well as the potential suffering to the animals. This kind of analysis allows for nuance and flexibility based on facts on the ground. In this situation, it seems to me that the ban should be rescinded and replaced with a more tailored approach that includes the human element.

Yet more squabling over the family album.

Homo naledi as Spin Detector:
 Ann Gauger September 13, 2015 12:28 PM

You have probably seen the headlines. Numerous fossils of a new species of hominin have been found in a nearly inaccessible cave in South Africa. Intriguingly, the fossils appear to be part of a very large deposit of bones, apparently left there deliberately by their own kind. Also intriguingly, the skeletons of these individuals may have some traits that are Homo (human-like) and some that are australopithicine (more ape-like). To add further to the mystery, these fossils may be anywhere from 1 to 3 million years old, potentially making them among the oldest fossils identified as being of our genus Homo.

In reading the coverage of Homo naledi, as the species is called now, it seems clear to me that the spin put on the actual bones depends on the assumptions of the writers. What do I mean? Bones can only tell us so much. The rest is a matter of interpretation, and one's point of view inevitably tends to color that interpretation.

Let me give two examples:

The first example is how writers interpret skull size. H. naledi had a small brain compared to ours, about the size of a chimpanzee's. To some writers that seems to indicate the probable lack of high levels of cognition. Only species with brain sizes near our own are considered intelligent. The data used to support that claim are (a) our current knowledge of chimp and gorilla brain sizes, and their lack of rational, abstract thought; and (b) the claim that a gradual progression in brain size exists from australopiths to Homo erectus to Neanderthals to us, indicating a gradual progression in intelligence, which fits the evolutionary story.

There are two problems with these interpretations. First, modern humans exhibit a range in brain sizes, and those differences do not correlate with intelligence. The fossil skulls of Homo erectus, the earliest fossil judged to be "human," exhibit a range in skull size also (but see Casey Luskin's post on Homo habilis). Second, if we were to judge intelligence based on brain size, Neanderthals would be smarter than us since their average brain sizes were more than average human brain sizes. Maybe they were smarter?

H. naledi has a mixture of ape-like and human-like traits. It depends on the desired outcome which traits will be emphasized, and where H. naledi will be placed on the putative fossil tree. The discoverers have placed her squarely on the human side based on her apparent behavior and her inferred ability for long distance walking.

By her apparent behavior I mean the fact that the deposit of bones was found deep in a lightless cave with difficult access. It would take much effort and perhaps some light to make the journey. Yet many, many individuals were found in that dark cave. The discoverers, chief among them Lee Berger, have claimed this as evidence of human intelligence. Such deliberate behavior required significant effort and some danger and indicates a special care for the dead, something that until now only humans were known to exhibit. (I am counting Neanderthals as human.) Yet there are those who seek to claim this is not evidence of ritual behavior or a special care for the dead, that it may be a form of animal behavior. I suspect these people may find the small skull size more significant than the behavior, or they have some other driving motivation for discounting it. Not everyone wants to find evidence of human intelligence and care for the dead in fossils so old or in brain sizes so small, and not everyone likes Lee Berger.

To quote a piece on PBS:

[William] Jungers, [chair of the department of anatomical sciences at Stony Brook University], doesn't dispute that the H. naledi bones belong in the genus Homo and were likely deposited deliberately, but he cautions against "trying to argue for complex social organization and symbolic behaviors." There may be a simple answer. "Dumping conspecifics down a hole may be better than letting them decay around you." He suggests it's possible that there was once another, easier, way to access the chamber where the bones were found. Until scientists can know the approximate age of the Homo naledi fossils, Jungers says they are "more curiosities than game changers. Intentional corpse disposal is a nice sound bite, but more spin than substance."
Jungers is more dismissive of Berger's suggestion that we may have inherited the practice of burying our dead from H. naledi, a creature with a much smaller brain than modern humans. "That's crazy speculation -- the suggestion that modern humans learned anything from these pin heads is funny."

So back to the small skulls. The two opposing views must argue that either (a) behavior does not correlate with intelligence because skull size trumps everything, or (b) behavior correlates with intelligence and skull size doesn't matter. In addition, behavior and intelligence trump other differences in morphology. True human status is assigned regardless of shoulder and pelvis shape, or the as yet undetermined age of the fossils.

Even the way H .naledi is described by science writers reflects a certain bias. The disagreement is not due to scanty evidence but rather to interpretation. Some emphasize that the hands are more chimp-like in their fingers, and that the shoulders appear to be suited for climbing. Thus H. naledi spent time in trees, making her more australopith-like. Others emphasize that limbs and feet appear to be mostly like ours, indicating long distance walking ability, and thus assign her status as Homo.

In fact there is a dispute about whether the find represents one species or two. Berger and his coauthors claim the find represents one species. But others disagree. Jeffrey Schwarz, professor of biological anthropology at the University of Pittsburgh, says this about Homo naledi and the subject of classification and preconceived notions:

...How do paleoanthropologists decide if a specimen belongs to a species - whether newly or already named - and if that species is a member of Homo? As the case of Homo habilis illustrates, it is primarily by chronology, not detailed morphology...
Enter the newly announced species, Homo naledi, which is claimed to be our direct ancestor because it has features of australopiths and Homo. Why is it a species of Homo? Because some specimens seem to be like us. Why australopith? Because other specimens have some of their features. Why do all belong to the same species? Because they were found in the same cave. but, the published images tell a different story.... Even at this stage of their being publicized, the "Homo naledi" specimens reflect even greater diversity in the human fossil record than their discoverers will admit.

What to do? As I recently advocated in the journal Science, it's about time paleoanthropologists acknowledged what a taxonomic and undefinable mess the genus Homo has become, and restudy the human fossil record without preconceived notions and the historical weight of overly used names.

In the interests of fairness, as far as I know neither Junger or Schwarz has examined the actual fossils first hand. So to give Berger and his extensive list of coauthors their chance to speak (Berger has welcomed the collaboration of many experts in their fields) I quote from their paper defining the species:

In addition to general morphological homogeneity including cranial shape, distinctive morphological configurations of all the recovered first metacarpals, femora, molars, lower premolars and lower canines, are identical in both surface-collected and excavated specimens ....These include traits not found in any other hominin species yet described. These considerations strongly indicate that this material represents a single species, and not a commingled assemblage....
The collection is morphologically homogeneous in all duplicated elements, except for those anatomical features that normally reflect body size or sex differences in other primate taxa.


This is a very interesting fossil find. I am sure what it means will be argued over extensively in years to come, as more data is collected and analyzed. However, the undisputed bias will undoubtedly be that the evolutionary story of our common ancestry with chimps is true, regardless of where H. naledi is assigned in the story.

Is our planet privileged by chance or choice?

Rare Earth Redux: Design Inference, Anyone?
Evolution News & Views September 14, 2015 3:41 AM

Something else that is special about planet Earth has been noted: its mineral content, compared to other planets. Robert Hazen, an origin-of-life researcher at the Carnegie Institute, states in an article posted by NASA's Astrobiology Magazine that Earth's mineral abundances may be unique in the cosmos. There were only a dozen or so minerals present at the birth of our solar system, he argues, but there are about 5,000 types today. Most of these, he says, can be "linked directly or indirectly to biological activity."

That much Hazen and his team knew a decade ago. Now, they have taken the concept of "mineral evolution" further, determining the probability of mineral distributions:

They discovered that the probability that a mineral "species" (defined by its unique combination of chemical composition and crystal structure) exists at only one locality is about 22 percent, whereas the probability that it is found at 10 or fewer locations is about 65 percent. Most mineral species are quite rare, in fact, found in 5 or fewer localities.
"Minerals follow the same kind of frequency of distribution as words in a book," Hazen explained. "For example, the most-used words in a book are extremely common such as 'and,' 'the,' and 'a.' Rare words define the diversity of a book's vocabulary. The same is true for minerals on Earth. Rare minerals define our planet's mineralogical diversity." [Emphasis added.]

How does this intersect with intelligent design? The minerals could be byproducts of microbial activity, not intelligence. Still, it's intriguing that life as we know it depends on a seemingly un-natural distribution of minerals.

Further expanding the link between geological and biological evolution, Hazen's team applied the biological concepts of chance and necessity to mineral evolution. In biology, this idea means that natural selection occurs because of a random "chance" mutation in the genetic material of a living organism that becomes, if it confers reproductive advantage, a "necessary" adaptation.
But in this instance, Hazen's team asked how the diversity and distribution of Earth's minerals came into existence and the likelihood that it could be replicated elsewhere. What they found is that if we could turn back the clock and "re-play" Earth's history, it is probable that many of the minerals formed and discovered in this alternate version of our planet would be different from those we know today.

This is why Hazen believes Earth's mineral signature is "unique in the cosmos." His idea resembles Stephen Jay Gould's notion that re-playing the tape of life would produce a very different menagerie of creatures.

What must strike any astrobiologist with amazement, though, is how many elements and minerals vital to life exist near the surface of the earth. The abundant elements -- carbon, hydrogen, nitrogen, oxygen -- are not that surprising. But life as we know it requires other elements that are less common: potassium, phosphorus, magnesium, calcium, selenium, sulfur, and even chlorine.

That's why the typical astrobiological speculations about life on other planets, such as this evidence-free press release from Washington State University, are misleading. WSU planetary scientist Dirk Schulze-Makuch speculates about "what life could be like elsewhere in the universe" with thoughts about what might exist on Mars or Titan. Has he performed an elemental analysis of the minerals available on those worlds?


The unique availability of so many elements and minerals at the surface of the Earth could merit a design inference, when considered in addition to all the other factors that make it habitable, as discussed in The Privileged Planet. Astrobiology, like SETI and SEETI (see "Extinct Aliens Could Yield a Design Inference"), despite their confidence in Darwinism, end up making pretty good cases for intelligent design.