On Saturday someone yelled at me following a Science Festival Event. It was a talk presented at a meeting of the Philadelphia Association for Critical Thinking(PhACT) and the scientist giving the talk, Dave Cragin, is a friend. His talk was informative and interesting but I thought he was a tiny but unfair to the press and asked him to clarify one point.

As an example of bad journalism he’d held up a dishonest press release that was put out by an environmental group. Another example of misleading reporting came from Environmental News Network, which is not a journalistic publication but some kind of collaborative effort among environmental groups.

So I just mentioned that if he wanted to criticize the press, he should have at least one example from the press. I asked if he’d seen similarly irresponsible content in the New York Times or the Philadelphia Inquirer. From somewhere behind me a woman cackled, “Are you kidding, they’re hideous!” I found out later she is a scientist.

Dr. Cragin agreed with me later that he should be more specific in his criticism. I explained to him that PR and journalism stem from different motivations. PR is a form of advertising. The goal is persuasion. Journalists are supposed to aim for the truth. We don’t always succeed but we try.     

This is the second time in one week I’ve witnessed scientists accusing the press of stupidity, gullibility or dishonesty and then holding up as evidence a press release that came from an interest group, university or a scientific organization.  

Today’s column profiles some Penn-led research into the DNA of African Pygmies. To me, the most interesting part of the research project is the way it dispels a prevailing mythology about genetics. Much of that mythology took root when scientists were trying to sell the public and Congress on the $3 billion Human Genome Project. They promised that reading the sequence of code characters in human DNA would lead to cures for cancer, Alzheimer’s disease, cardiovascular disease, mental illness, and autoimmune diseases.

It’s true that the genome has been a useful tool for researchers whose work is improving human health. But where are the cures? In all those promises that went with genome promotion, there was the implication that death was caused by faulty genes. We would live forever if not for little genetic time bombs that would explode and clog our arteries or start tumors. Genome hype also led to myth that our DNA would reveal everything about us. A few were honest about the fact that it wouldn’t be so simple.

One of the early outspoken skeptics was Ken Weiss of Penn State, who was quoted in this story. It reveals the reality that confronts scientists when they try to find the genetic causes behind even seemingly simple traits. Here's the column:

Scientists who study human evolution have long puzzled over why African Pygmies are so short.

It is one of the most visible examples of human diversity, with Pygmy males standing just 4-foot-11 on average, while some of their neighboring ethnic groups are tall. Many biologists have assumed there must be some direct evolutionary advantage to their short stature — perhaps that they better maneuvered through the forest or they survived on less food.

Immunobiologist Ruslan Medzhitov said he was recently discussing evolutionary medicine with fellow Yale professor Stephen Stearns, and Stearns told him that patients often like evolutionary explanations for their ailments. “It helps them with the ‘why me’ question,” Medzhitov said.  

Medzhitov is known for his pioneering work on the so-called innate immune system, for which many think he should have shared a recent Nobel Prize. Now he’s turned his attention to the evolutionary roots of allergies. This week he’s lead author on a Nature paper that could help Higgs and other allergy sufferers with that “why me” question. Allergies are not just a malfunction of the immune system, he said. They may also reflect an evolutionary battle between us and the many species that surround us.

The standard theory holds that allergy evolved as a mechanism to help us and other mammals fight parasitic worms, he said. He proposed that allergic symptoms also evolved to help animals to avoid venoms and other noxious chemicals in the environment.  Most allergy symptoms function to either expel something or make us run the other direction, he said.  We humans vary in how strongly we react and what we react to, but it’s all part of a system for keeping us from being damaged by toxins and irritants.

He offers a possible explanation for why severe allergies are on the rise – we’re increasingly living in enclosed spaces. For most of our evolutionary history, people weren’t exposed to peanut dust in an airplane cabin, or to dust mites in a bedroom. Now, however, we live in enclosed spaces where there’s no turning away. Higgs suffers from skin rashes that have been diagnosed as allergies. The veterinarians put him on a diet of hydrolyzed protein to no avail. They shaved his fur and scratch tested his skin but got no definitive answers. He’s fine with the occasional anti-inflammatory steroid pill. He was probably fine when he lived out in the alley, but he has no desire to return.   

F.F. I'm thinking about giving Higgs a chance to co-blog every Tuesday. Here are some of his most recent thoughts about evolution.

Higgs: After some months of co-blogging on the subject of evolution, I’ve learned that humanity has a strange obsession with finding those traits that render you uniquely human – qualities that you hope will set you apart from all the other animals. In search of those defining traits, you’ve considered self-awareness, consciousness, artistic expression, tool use, language, empathy, self-discipline, capacity for planning, fear of death, and the preference for grilled meat over raw.  

Some of these traits are not shared by all humans. And some are shared with other animals.

I’ve come to suspect that you humans are misled by an unconscious desire to tie uniquely human traits with those qualities you most value and desire to cultivate in yourselves. That’s a false connection. Your best human traits may very well be ones you share with other species. Many of you, for example, value the ability to give and receive love as one of the loftiest capacities of the human soul. This is not only within my ability but the essence of my job description.

My love was hard-earned and required months of patience because my roots are feral and human beings once terrified me. Now, however, I have opened my heart to a once alien species and I bring joy and delight to all who touch me.

FF: Someone wiser than I am once told me it's better not to argue with irrational people. That's usually true, but not always. At this point I'm turning the post over to my co-blogger Higgs.

Higgs: Hi people. Higgs here. I wanted to share this video which shows one of my favorite humans, Stephen Colbert, toying with a creationist the way a cat would play with a mouse before devouring it. Colbert’s swipes are so quick and skillful that his prey isn’t even sure he’s being eaten for breakfast. Enjoy.  

Despite the fact that we can’t see oxygen or carbon dioxide in our air, the existence of these invisible gases is not a radical theory but a well-established science. Back in the 1800s, physicist Michael Faraday used a series of experiments involving a candle flame to show children how to reveal such otherwise invisible gases. He also demonstrated how different invisible gases behave quite differently from one another. Some fed flames, for example. Some extinguished them.

I thought about Faraday’s lectures when I read this story over the weekend in the New York Times, describing a controversy that surrounds a Discovery Channel documentary about the Earth’s polar regions.  

According to the story, the film is full of visual evidence for melting glaciers, shrinking sea ice and threats to wildlife. And yet, there’s a conspicuous absence of any mention of carbon dioxide or other greenhouse gases as probable causes:    

The vast majority of scientists agree that human activities are influencing changes to the climate — especially at the poles — and believe that the situation requires serious attention. That scientific consensus is absent from “Frozen Planet,” for reasons that shed light on the dilemma of commercial television, where the pursuit of ratings can sometimes clash with the quest for environmental and scientific education, particularly in issues, like global warming, that involve vociferous debate.

Including the scientific theories “would have undermined the strength of an objective documentary, and would then have become utilized by people with political agendas,” Vanessa Berlowitz, the series producer, said in an interview.

The relevance of evolution to the origin of life came up in the comments following yesterday's post. That may not be a coincidence, since I had been working on this piece at the time and talking to scientists who envision the origin of life as an evolutionary process. How could "chemical slop" become life? A closer look reveals that some chemicals are not as sloppy as they appear to the untrained eye.  

This column will also a appear in Monday's Inquirer:

Blurring the lines between life and inanimate matter, biologists announced today that they’d created six different chemical alternatives to DNA and coaxed them to undergo evolution.

A description of these code-carrying molecules, called XNAs, was published in the journal Science. The work bolsters a prevailing hypothesis that life as we know it evolved from simpler life forms, no longer here, and those evolved from something simpler. There may be no moment when the first life emerged, but instead an evolutionary process by which chemicals that most of us would consider non-life gradually gave rise to living cells through natural selection. 

The work on XNA molecules adds to a growing field of test-tube evolution, in which scientists are nudging code-carrying chemicals to evolve into drugs or other useful compounds.

It’s not only members of the religious right who go around saying science is a form of faith. I just found out from the blog Cosmic Variance that Jon Stewart has made similar claims on his show. Stewart uses antimatter as an example of something scientists just believe in, despite our inability to see it. Read the post and watch the clip here.

Here’s what Stewart has to say about faith and science:

"I’ve always been fascinated that, the more you delve into science, the more it appears to rely on faith. You know, when they start to speak about the universe they say, well, actually, most of the universe is antimatter. Oh, really, where’s that? Well, you can’t see it. [Robinson: "Yes, exactly."] Well, where is it? It’s there. Can you measure it? We’re working on it. And it’s a very similar argument to someone who would say God created everything. Well where is he? He’s there. And I’m always struck by the similarity of the arguments at their core."

My first reaction is that Jon Stewart must be kidding around, but he seems to be serious. He isn't playing a character the way Colbert does. It’s sad if Stewart really thinks physicists just make up things like antimatter. Positrons are so well-established they are used in medicine. Physicist Sean Carroll addresses Stewart’s strange assertion. In his blog post, Carroll assumes Steward probably meant dark matter since nobody is claiming most of the universe is antimatter. Either way, Stewart is missing something important about the nature of science:

Obviously he means something like “dark matter,” not “antimatter,” but that’s a minor mixup of jargon. Much worse is that he clearly has absolutely no idea why we believe in dark matter — what the actual evidence for it is in real data. He betrays no understanding that we know how much dark matter there is, have ongoing strategies for detecting it, and spend a lot of time coming up with alternatives and testing them against the data. What kind of misguided “faith” would lead people to believe in dark matter, of all things? (The underlying problem with appeals to faith is that they cannot explain why we should have faith in one set of beliefs rather than some other set … but that’s an argument for a different day.)

Yesterday I was trying to find something interesting to say about the second Philadelphia Science Festival, which starts this weekend. I asked one of the spokespeople what the purpose of the festival was supposed to be, and he said it’s intended to get young people interested in becoming scientists.

Seems worthy, but do we really need more scientists or fewer? Or do we just need more good scientists? One thing we don’t need are more bogus scientific papers. Yesterday’s New York Times had an interesting story about a rise in retractions, and among the many reasons cited for the glut of bad science was a glut of wannabe scientists.

The so-called high impact journals – Science, Nature and the New England Journal of Medicine – have the worst record when it comes to retractions. The article quotes an editor of Science with an excuse:  

Monica M. Bradford, executive editor of the journal Science, suggested that the extra attention high-impact journals get might be part of the reason for their higher rate of retraction. “Papers making the most dramatic advances will be subject to the most scrutiny,” she said.

Another possible explanation is that these journals gravitate toward the kinds of results that go against conventional wisdom and are so surprising that they can become potential cocktail party tidbits for the general public.