Animal speech

I know that animals vocalize but do they have an internal language? Something like what you experience now as you read this? Since animals don’t write articles in which they wonder about speech in humans, we can only infer from observation.

Koko jas sign language

Koko has sign language

Getting inside the heads of animals requires time and patience. Francine “Penny” Patterson has spent years in a California zoo teaching Koko, a gorilla, sign language. Koko can name hundreds of objects.

Still, gorillas don’t talk to each other. Anthropologist Holly Dunsworth notes: “Gorillas grumble in the presence of large amounts of food, they grunt as they approach one another or separate from their young, they make copulatory grunts, and they chuckle when they play (Scientific American January 1, 2016).” The vocalizations that gorillas make are no more complex than their visual displays. They telegraph social status and possible behavior, but that is all.

Vervet monkeys do better. They make distinct predator alarm calls for “eagle,” “snake” and “leopard.” Unlike Koko, no human taught Vervets these “words.”   Even then, Vervets don’t have conversations about the big snake they saw yesterday.

Animals appear to lack abstract reasoning: the ability to transfer knowledge from a one situation to one that hasn’t yet happened.

Crows seem to have abstract reasoning. They will drop walnuts to a hard surface and crack them open. They seem to be thinking “if I drop this nut from high enough to the hard concrete sidewalk, it will break open.”

A more likely explanation involves an observation about ourselves than about animals. We tend to anthropomorphize: to view the world of animals through our own eyes. We visualize them with human-like language and intentions.

Sara Shettleworth, cognitive scientist at the University of Toronto says that “proximate cause” is a better explanation. In biology, proximate cause is the most immediate cause of an event. The crow didn’t drop the walnut because it was thinking about the hardness of nuts relative to the sidewalk, the distance it had to fall, and the consequences of the impact.  No, the bird’s physiological state was a key factor. Hunger linked to the walnuts and hard surfaces.

“That is, physiology that encourages conditioned food-procurement behavior based on past success is what causes a crow to fly above hard surfaces and drop nuts, not the crow’s logic about how to best satiate its hunger,” explains Dunsworth. If the crow hadn’t accidently seen how well the technique worked, it wouldn’t have come up with the behaviour based on analysis.

It’s an honest mistake. If we have abstract reasoning, our natural inclination is that animals do: we project our view of reality on to the world.

I don’t mean to suggest that human animals are superior, just different. The mental baggage we carry comes at a cost. It may help us construct our world to tell ourselves: “Take this saw and make a table.” But those voices can also appear to be external and malicious, as in schizophrenia, and tell us: “Take that screwdriver and stab the devil Fred through the heart” –an internal voice I’m quite sure animals don’t hear.

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When is a GMO not a GMO?

Everything we eat has been genetically modified but no one would call crops from common crossbreeding GMOs. No, Genetically Modified Organisms occur when DNA from one species is inserted another. So-called transgenic crops, such as corn and soybeans, are resistant to the herbicide Roundup. Use of the technology has led to public distrust of GMOs.

crossbreeding

But other technologies modify genetics yet they are not defined as GMOs. With the arrival of the precision gene-editing tool called CRISPR, definitions become more than just semantic says Scientific American (March, 2016). If the foods produced by CRISPR are not defined as GMOs, then public acceptance will be greater.

Let’s look at some current technologies that are not defined as GMOs. The oldest is conventional crossbreeding, widely regarded as “natural.” If we want a blight-resistant plant that produces desirable fruit, a wild relative of the plant that is blight-resistant can be cross-pollinated with one that produces desirable fruit. However, this process is not precise –it transfers not only the desirable trait but also large segments of chromosomes. Along with the desirable chromosomes can be undesirable ones; a process called “linkage drag.”

Modern wheat is one of those. Nina Fedoroff, a plant biologist and former president of the American Association for the Advancement of Science, refers to domesticated versions of bread wheat created by traditional breeding as “genetic monstrosities.”

Then there is Mutagenesis, not considered as creating GMOs by the U.S. Department of Agriculture. Developed in the 1920s, it involves the use of x-rays, gamma rays or chemicals to induce mutations in plants. The mutants are ten examined for desirable traits. It’s a shot in the dark.

A more precise shotgun approach was refined in the 1980s. Cisgenesis involves using a DNA particle gun to literally shoot genes with the desirable trait into a plant cell. Cisgenesis can also be accomplished by using bacteria to carry the desirable genes into the plant cell. It’s more efficient than conventional crossbreeding because there is less linkage drag. Whether or not the product is a GMO is determined on a case-by-case basis.

Gene-spliced plants are not considered GMOs. In this method, undesirable traits are turned off by introducing RNA into genes which interferes with the gene. Some approved foods using this method are non-browning potatoes and apples.

CRISPR is totally new and the jury is out on whether they produce GMOs or not. The precision and low-cost of CRISPR confound the problem. As I described in an earlier column, CRISPR is like a search and replace function in a word processor in which all instances of a spelling error can be found and replaced.  Or it can be used to find and simply delete the error.

Supporters of CRISPR argue that when the technology is used to delete but not insert genes, then the results should not be called GMOs: as when an undesirable trait is deleted and not replaced with anything.

Critics of CRISPR say that any tinkering with genes using any technology, other than “natural” methods, should be enough to label the products as GMOs.

Clearly, public acceptance relies on accurate definitions.

 

The promise and peril of CRISPR gene technology

So far, the promise of genetic engineering to cure disease has been a bit of a dud. Up until now scientists could only read our genomes – now they can write. A gene-editing tool found in bacteria, called CRISPR, is poised to achieve that goal.

CRISPR

As well as read, the old technology allowed the ability to add says Dr. Elizabeth Simpson at the University of British Columbia on CBC Radio’s Quirks and Quarks. She’s begun to use CRISPR in her work on aniridia, a genetic eye disease.

“In the older technology we would add the missing gene, not insert it into the genome to make the eye function properly. We had a lot of trouble making the addition produce the right amount of protein at the right time. With CRISPR, all the natural regulation is still there and can be used by the eye to heal itself. We don’t have to be as clever and it’s a faster way to go.”

CRISPR (Clustered regularly-interspaced short palindromic repeats) is part of a natural bacterial defense. Scientists have known about these sections in bacterial DNA for years but they didn’t know what they were for or how they got there.

Then they discovered that these repeated clusters were sections of DNA gathered from attacking viruses: the bacteria had literally incorporated the enemy’s DNA into theirs. Still, their function remained a mystery.

Dr. Sylvain Moineau, Professor at the University of Laval, was one of the researchers to find out. He discovered that some yogurt bacteria weren’t susceptible to viral attack and some were. The ones that weren’t used the embedded viral DNA, described above, as a natural defense. These successful bacteria compared the embedded viral DNA with sections in the attacking viruses, and then cut that section out. As you can image, viruses don’t work well with gaping holes in their midsections: a pretty good defense.

While cut up viruses don’t work well, human DNA has the ability can stitch itself back up. That allows CRISPR technology to remove parts of our DNA that cause disease and replace it with functioning parts.

That’s the wonder of CRISPR. It cuts out the bad parts and inserts the good parts. Think of it as the search and replace function in word processors says Dr. Feng Zhang at the Massachusetts Institute of Technology who was key in transforming the natural CRISPR system into a gene editing tool. For example, if I’ve misspelled CRISPR throughout this whole article, I can use the search and replace function in Word to replace all incorrect instances of CRISTR with CRISPR.

Powerful tools in the hands of the wrong people can be disastrous. It would be wonderful to cure muscular dystrophy and Huntington’s disease. And since permanent genetic changes can be passed on through generations, malaria could be wiped out forever by making mosquitoes resistant to the parasite.

But In the hands of bio-hackers and unethical corporations, CRISPR could wreak havoc in areas of agriculture, biology, pharmaceuticals, ecology and wildlife preservation.

Ethical debates must take place before the technology becomes widespread. It’s another reason that we need strong government regulation.

How science works

Scientists overwhelmingly agree that humans are contributing to global warming in a significant way: 97 per cent of tens of thousands of scientists from a variety of disciplines are convinced of anthropogenic global warming (AGW).

induction-deduction-1

But consensus alone doesn’t make it true. Albert Einstein make that point in 1931 when a book was published renouncing his theory of relativity. The title, “100 Authors against Einstein,” said it all.

Einstein replied: “Why 100? If I were wrong, one would have been enough.” His point was that consensus does make a scientific fact. He wasn’t right just because he was Einstein. He was right because thousands of scientists found that he was right.

Revolutionary ideas aren’t necessarily true but many are. Michael Shermer, publisher of Skeptic magazine, lists some:

“The Copernican model, germ theory, the vaccination principle, evolutionary theory, plate tectonics and the big bang theory were all once heretical ideas that became consensus science. How did this happen?”

It didn’t become true based on the results of a poll. The results of a poll done in 2011 by Associated Press-GfK showed 77 per cent American adults believe in angels.

By the consensus model alone, angels exist. Both the majority scientists who believe in AGW and the believers in angels must be right. However, if we apply the test of consilience, one belief tumbles. Consilience is defined as the linking together of principles from different disciplines to form one comprehensive theory.

The 19th-century philosopher of science William Whewell argued for a “consilience of inductions.” Inductive reasoning is defined as that which derives general principles from specific observations.

“For a theory to be accepted, Whewell argued, it must be based on more than one induction—or one single generalization drawn from specific facts,” explains Shermer. “It must have multiple inductions that converge on one another, independently but in conjunction.”  Call it a convergence of evidence.

Whewell wrote in his 1840 book: “Accordingly the cases, in which inductions from classes of facts altogether different have thus jumped together, they belong only to the best established theories which the history of science contains.”

The flaw in the belief of angels is that inductive reasoning isn’t used, let alone the more rigorous test of consilience. To meet the standard of consilience for angels, not just one generalization from many facts must come about, but many generalizations must come together.

One the other hand, it’s not difficult to study whether climate change is caused by humans. That’s because there is a convergence of evidence from multiple lines of inquiry—pollen, tree rings, ice cores, corals, glacial and polar ice-cap melt, sea-level rise, ecological shifts, carbon dioxide increases, the unprecedented rate of temperature increase—that all converge to a singular conclusion.

So, what about the three per cent of scientists who don’t believe in AGW? Perhaps they, being in the minority like Einstein was, are right. But they fail the test of consilience and have a number of flaws including cherry-picking, curve-fitting, and disregard for inconvenient data.

“That is, instead of the 3 percent of papers converging to a better explanation than that provided by the 97 percent, they failed to converge to anything,” says Shermer.

How to market sugar water

There’s no doubt that consumption of pop is harmful, even deadly but you’d never know it from the soft drink industry. Professor Paulette Nestle, nutritionist at New York University, is blunt:

“The science is clear. Kids and adults who drink pop tend to be heavier and have a higher prevalence of obesity, type 2 diabetes, heart disease, and tooth decay.”

coca_cola_bubbles

Studies funded by the soft drink industry find the opposite: roughly 85 per cent of them find pop to be harmless. And if there is a problem, they say, it’s your fault. No one is holding a gun to your head and forcing pop down your throat. The problem lies on the shoulders of individual consumers. It’s a matter of choice. If only consumers would exercise more.

However, consumers make choices on what they perceive about a product and the sugar water industry is persuasive. They spend millions of dollars on Super Bowl ads that avoid the product itself. Instead, they market deep emotional connections to friends and family. If I can find happiness in a can of Coke, why wouldn’t I drink it?

And if I can find my identity in a can of pop, all the better. Coke sells cans with my name on it and words such as Love and Superstar. Who wouldn’t want to support a corporation that supports the arts, community projects, and cleaning up the environment?

“When Philadelphia was considering a soft-drink tax, Coke offered to give the Children’s Hospital of Philadelphia $10 million. It’s that kind of thing,” says the author of eight books in a newsletter from the Centre for Science in the Public Interest.

It’s a standard tactic used by the merchants of misery. You see it used by proponents of Ajax mine in Kamloops. They don’t address the problems that the mine will create: like toxic dust, groundwater contamination, potential sludge spills, the environmental headache created by the mountain of tailings when they leave.

No, Ajax mine tells us how important copper is to our daily lives, how they will create jobs, how they support our university and the arts. To oppose the mine is to oppose family and community, they would have us to believe.

The sugar water industry has learned from the tobacco industry that you can counter science by creating doubt. Sure, 99 per cent of studies might find that consumption of tobacco causes cancer but if only one study is inconclusive, then maybe tobacco is not that bad. It’s human nature to hope that something we want will be OK despite mounting evidence to the contrary, something we are addicted to or feel a deep emotional connection to, something that will create jobs.

Another tool in the toolbox is to fund groups like the Global Energy Balance Network. The group employed scientists of considerable stature who found that lack of exercise, not diet, was responsible for the obesity epidemic. Then a reporter for the New York Times discovered that these scientists had been taking millions of dollars in research grants from Coca Cola including funding of the website.

One of these scientists said not worry about eating less, gobbling junk food, drinking pop. Just be more active. Would it were true.

Einstein misunderstood

Einstein was misunderstood when he said that God does not play dice with the universe. Philosophers assumed that Einstein was asserting that events don’t occur randomly; that the universe is one giant clock unwinding; that everything we think, every action we take, is predetermined at birth; that we are essentially meat machines.

roll-the-dice

Einstein believed no such thing. Not only is such a claim contrary to Einstein’s theories, it violates our common sense view of free will. I can continue to read this, or not. And free will is fundamental to law. Any crime I commit is not my doing; it is simply predetermined, out of my control, not my fault.

Einstein’s comments were directed towards the “Copenhagen agreement” in which Erwin Schrödinger wrote a wave function that predicted where you are most likely to find particles, such as the location of electrons around an atom. The function determines the probability of finding particles. Science writer George Musser describes Schrödinger’s function as a “haze of potential existence.” Mysteriously, when the wave function “collapses”, particles spring into existence by merely observing them.

“When you so much as look at a particle – bam! –its stops behaving deterministically and leaps to an end result like a kid grabbing a seat in musical chairs. No law governs collapse. There is no equation for it. It just happens.”

Einstein had trouble with that concept. He reasoned that there must be some underlying mechanism; that particles don’t spring into existence at the roll of the dice. What does it mean to observe something, anyway? Would a mere glimpse do? Could cats and bats bring particles into existence by observing them?

Einstein’s had no answer to his question. He simply said that there must be more to it than that. He believed that a branch of physics called statistical mechanics might hold the answer. It hypothesizes that events happen in both a completely random yet perfectly predictable way depending on the level of examination.

Einstein knew that things appeared to happen in a random way. But that even the unpredictable decay of radioactive nucleus must be predictable at some underlying level. That was Einstein’s complaint and what the Copenhagen agreement failed to explain.

To imagine how systems at different levels operate independently, imagine a hockey puck racing towards a goalie. At the level of atoms, the action seems completely random yet the flight of the puck is perfectly predictable (while scoring may not be).

Or imagine the opposite: that some demon could calculate the trajectories of the billions of atoms in dice as they are rolled. Even if all the details are known at the atomic level, the outcome is still a statistical prediction. The probability of each die landing on any side is one out of six.

Choice has nothing to do with atoms. It has to do with desire, intention, possibility –which exist at the psychological level of living, breathing humans. Why did you chose to read this far? Because you wanted to.

“My desire explains my action,” concludes Musser, “Most of the times that we ask ‘Why?’ we are seeking someone’s motivations rather than the physics backstory.”

100 years of Einstein

This month, one hundred years ago, Einstein completed his theory that would forever change physics. Not just physics but his astonishing ideas revolutionized philosophy, art, and culture. A commemorative issue of Scientific American is unambiguous on his impact: “How Einstein reinvented reality.”

elevator-buttons

Before Einstein, gravity was thought to be a force that pulled coffee cups to the floor. I remember the terse graffiti written on a washroom wall that summarized this notion: “gravity sucks.”

Einstein was sitting in a Swiss patent office in 1907 when a thought “startled” him. He recalled: “If a person falls freely, he will not feel his own weight.” We all have fanciful thoughts but this one had serious implications.

In his thought experiment, Einstein imagined a person falling in an elevator. Our office worker only wanted to get off on the third floor and now he’s falling, weightless, to certain doom.

But no, Einstein now imagines our hapless worker, in his elevator, floating in space. Unless the clerk was told, he would be unable to tell the difference because in both cases he is weightless. While floating in space, free as stardust, is a better choice, he’ll still have some explaining to do.

Einstein’s genius was equating the two and called it “the equivalence principle”; both merely manifestations of the same phenomena.

Einstein then turned to another thought experiment. Now he imagined our worried wanderer accelerating upward through space, the floor pushing up on his feet. By the equivalence principle, our reluctant spaceman could easily imagine himself safely back on earth waiting in his elevator stopped between floors. But he is not.

Through a pinhole in the wall, he sees beam of sunlight. To his astonishment, the beam doesn’t hit a point exactly opposite the wall but slightly lower. Because he is being accelerated, by the time the beam hits the opposite wall the elevator has moved up.

Fine, but what could possibly cause that to happen back on earth? It turns out that space itself is curved and that light beams follow those curvatures, as does everything else. Massive objects create dents in space somewhat like a bowling boll dents a trampoline. Rather than “fall,” objects follow those indentations in space.

Great ideas, but what about the math? Einstein’s brainwaves remained in the realm of speculation until 1912 when Einstein finally applied himself to the equations that would tie acceleration and gravity together. For four years he struggled with the math, often leading to dead ends. He told a fellow genius, David Hilbert, about his problem and Hilbert went to work on it too.

Einstein was under pressure. He promised a solution to be delivered to the Prussian Academy in November, 1915. Not only was he in a race to beat Hilbert to a solution but the clock was ticking down to the lecture.

After a month of whirlwind calculations and frenzied corrections, he arrived on November 4 still wrestling with his theory. “For the last four years,” he candidly told the assembled academy, “I have tried to establish a general theory of relativity.”

It was a long gestation and a difficult delivery but one which forever changed history. Meanwhile, our office clerk has some amazing stories to tell the kids.