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Any successful work of science fiction must succeed on two levels. First, it has to be entertaining: Most obviously, it must have enough cool special effects to bring in the kids and the fanboys. But second, it also has to make some interesting or provocative point about some larger issue: That will bring in the adults. That is, a good piece of sci-fi should be thrilling or chilling, and yet, at the same time, it must also be thought-provoking.

And so it is with “X-Men: First Class.” The film is based on a 50-year-old comic, but the SFX are totally 2011. And at the same time, the film brings a sharp eye to present-day issues, most notably the issues of tolerance and quality in a diverse society. Bullying? Intolerance? Prejudice? It’s all there to be noodled on, woven into a tale of mutants stretching from the Holocaust of World War Two to the nuclear fears of the Cold War. And if it’s easy enough to guess where a Hollywood movie comes down on the issue of gay tolerance, the film’s perspective on human evolution might be unnerving to many on the left, as well as the right.

The original “X-Men” was created in 1963 by Marvel Comics’ Stan Lee, who also created or co-created Spider-Man, Iron Man, and The Hulk.

Back in the early 60s, Lee intended “X-Men” to be a parable about racial prejudice in America. The X-Men (and Women) were a minority of mutants, and, as such, they suffered discrimination and alienation. But of course, they had superpowers, and so while they were sometimes shunned for their differentness, they were also feared for their power.

Thus the questions: Should mutants seek to blend in (integration), or should they seek to live by themselves, separate and apart from the larger society (mutant power)? Moreover, should mutants seek to improve society--or should they go to war against it?

Thereby hangs a half-century’s worth of tales--in comic books, cartoons, and, in the last decade, five separate movies. And because there are more than 100 “X-Men” characters--all with different powers--audiences never seemed to grow tired of them.

The new movie, which serves as prequel, tells the tale of how the first “class” of X-ers split into a good-guy faction and a bad-guy faction. And the backdrop of the film is the Cuban Missile Crisis--the actual historical event of 1962--enlivened by a storyline of hitherto unrevealed mutant involvement.

Yet the theme of the film--in between, of course, the stunts and explosions--is tolerance for difference. And so the new “X-Men” becomes a kind of coded meditation on the related themes of bullying and gay rights. Most of the major characters have a moment when they discover, to their visible relief, that they are not alone in their mutant-ness--others are like them.

These are themes similarly explored, to be sure, in the “Harry Potter” series; there, too, special kids must struggle with the realization that they are different, and they must choose whether or not to fit into, or fight, the larger society.

In the new “X-Men,” one mutant has been working as a super-smart nerd in a civilian job--when he is discovered to have feet that are like hands, so that he can grip on to things, upside down, like an arboreal mammal. When his feet-secret is finally revealed, he is asked, how did he get away with it? His answer: “Well, they didn’t ask, and I didn’t tell.” That, of course, is a play on the “don’t ask don’t tell” controversy in the U.S. military.

Perhaps the new film, most of all, is an argument against bullying. Thus “X-Men” picks up a vibe from the hit TV series “Glee”--and also, of course, from Lady Gaga, whose whole career bears witness (among other things) to the understanding and tolerance of difference.

Like a singing version of Oprah, Gaga has sought to “empower” her fans with a sense of their own unique identity; her recent song “Born This Way,” for example, is an ode to the the lonely and disrespected:

Whether life’s disabilities
Left you outcast, bullied, or teased
Rejoice and love yourself today
‘Cause baby, you were born this way

And then, of course, comes the anthemic pitch for equality of all kinds: “No matter gay, straight or bi/lesbian trans-gendered life/I’m on the right track, baby.” So perhaps while the kids are watching the X-ers zap each other on screen, the adults will be mulling over the film’s commentary on U.S. social policy.

Yet interestingly, over the course of the movie series, the X-ers seem less like underdogs and more and more like overdogs. As X-lore reminds us some 35,000 years ago, Neanderthal Man (homo neandertalensis) was muscled out of existence by Cro-Magnon man (homo sapiens).

“X-Men” imagines the next iteration of evolution: homo superior. And as one of the characters in the new film points out, when different species emerge, the newer species either eclipses--or outright destroys--the older species. In a real-world historical context, of course, such talk can be the stuff of genocide and race war; indeed, film starts off in a Nazi concentration camp.

Nazi murderers aside, human evolution is a touchy subject for many on all sides of the belief spectrum. Even the secular left gets nervous when the subject of human evolution, leading to human difference, comes into play.

Two decades ago, a book that argued that intelligence was partly of a function of genetics, "The Bell Curve: Intelligence and Class Structure in American Life," by Richard Herrnstein and Charles Murray, caused a political firestorm. Indeed, those fires still smolder today, flaring up sometimes when issues of school-testing and achievement scores arise.

Today, we know that human beings are indeed changing: We know that they are growing bigger and taller, and that, worldwide, they are getting smarter. Are such changes a function of better nutrition and health? Or is some sort of evolution still occurring? Meanwhile, who doubts that somewhere--in Silicon Valley, Singapore, China--visionaries and/or mad scientists in labs are plotting and scheming the next twist in the evolutionary spiral?

In the near term, scientists are likely to focus on what most folks would judge to be admirable goals for all: improving health, intelligence, and physical performance. Yet even incremental adjustments are likely to disrupt society.

And so what will happen if and when billionaires start getting visibly younger--beyond the capacity of plastic surgery, botox, and maybe human growth hormone? What will happen if genuinely upgraded people--or clones, or whatever--start appearing in our midst? Will we welcome the mutant newcomers? Or, to turn the question around, will the newcomers tolerate us and our continued existence?

Moreover, what will become of treasured notions about equality if we get to the point where genuine differences can be imprinted, demonstrated, even bar-coded? Will equality survive in a brave new world of built-in inequality?

Thus the paradox of the new film, and the whole of the “X-Men” saga. The intended message is harmony amidst difference, but the storyline is always discord, even violence, among visibly different factions. What does that tell us about the future of a speciated humanity?

Beyond the special effects, maybe “X-Men” is a already a hit (number 1 box office movie this past weekend) because it probes our deepest Darwinian feelings--and fears. If science succeeds in updating the definition of “fittest,” the survival of our particular species, in its current form, could be at risk. That’s great for future mutants, but not so great for the rest of us, and our current civilization.

So maybe “X” marks the spot where humans should start worrying.

James P. Pinkerton is a writer, Fox News contributor and the editor/founder of SeriousMedicineStrategy.