Politics are like markets – a struggle between the lizard brain and the cerebral cortex. The uproar over the sale of several U.S. ports to a company based in the United Arab Emirates is no exception.

Our collective lizard brain balks at the Bush administration’s approval of plan to let Dubai Ports World manage operations at harbors from New York to Miami. The collective cerebral cortex, that part of the national brain that does strategy, duly rebuts. On the Dubai Ports question, the lizard seems to be gaining ground.

You know the argument:

Lizard: Non-Americans shouldn’t control American ports.

CC: More than half of U.S. port terminals are already operated by foreigners. Non-Americans own 80 percent of the terminals in the port of Los Angeles, as a nice memo on the Council on Foreign Relations Web site points out.

Lizard: Memos are for people. Let the owner be a company from a safe country like Britain. A country that doesn’t produce terrorists. Even the name of the old company in charge makes me feel calm: Peninsular & Oriental Steam Navigation Co. of London.

CC: Come on. Shehzad Tanweer, who blew himself up in the London suicide bombings, was born in England. And P&O, the old British owner, will still be involved in managing the terminals. The only news here is that P&O has been acquired by Dubai Ports World.

Lizard: I still don’t want a United Arab Emirates company managing security.

CC: Dubai Ports won’t manage security. That job belongs to U.S. Customs and Border Protection.

Lizard: You didn’t hear me. I have trouble thinking of the United Arab Emirates as an ally.

CC: But the UAE is an ally. Our U-2 spy planes are based there.

Lizard: Chuck Schumer is right. This deal is too hasty. President Bush was caught flat-footed. Lizard smells opportunity for domestic political advantage.

CC: This deal was cleared by people lower down on the basis of old and explicit policy. The way President Bush reacted to the news of Dubai Ports World isn’t called “being caught flat-footed.” It is called “efficient delegation.” This fight is not about Bush. It’s about policy.

The dialogue goes on, with a few additional points coming from the challenged logical side. One relates to the Cnooc-Unocal debate of last summer. In that case, many Americans couldn’t get past the fact that Cnooc Ltd. was so closely linked to the Chinese government. The deal didn’t go through, and rightly so. To pretend that Cnooc’s offer for Unocal Corp. was merely about the free market was disingenuous. It was, arguably, not in the strategic interests of the U.S. for the Chinese government to control too much of the world’s energy.

The Dubai Ports transaction is different. This time, the deal ought to go through precisely because the Persian Gulf monarchy is involved. When we invite ambivalent allies like the United Arab Emirates or Pakistan into contracts like this one, we secure their friendship.

More interesting than the question of who directs containers onto a dock at Miami or New York is the question of why the lizard brain seems to be making such headway. Everyone from Charles Schumer, Democratic Senator from New York, to Dennis Hastert, the Illinois Republican and Speaker of the House, is criticizing the deal. President Bush, the never-veto president, is now saying he will use his veto to get the contract through. Why is old CC so challenged?

The answer is simple. Wars bring out the inner lizard in people. And the longer the war, the more powerful the lizard.

Next month brings the three-year anniversary of the Iraq invasion. If you reckon the current war as having started on Sept. 11, 2001, then you have a conflict that has lasted longer than U.S. participation in World War II. Americans are coming to a terrible realization: this is not a short war, or even a medium length war. It is a long war, like the Cold War.

Even as the president announced his justifications for the ports deal came news that Sunnis and Shiites were moving toward civil war in Iraq. Fight or flight, says the lizard. There are only two choices.

But that doesn’t mean that for the U.S. to succumb to either option would be constructive. The U.S. made a commitment to create allies in the Middle East, to trust them, and to work with them in a globalized world. The basis upon which the ports deal is moving forward dates to 2004’s Maritime Security Initiative, which said there should be cooperation “among nations and international organizations that share common interests.”

To say no to the ports deal is to abandon that principle – to say that a promise to other nations was just words. To say no is also to suggest that one can’t trust Muslim allies to have a visible physical presence in the U.S.

That in turn sends a strong signal that the U.S. really does draw an uncrossable line between itself and the non-Western world. Such a line means that the current war really will become, as Harvard professor Samuel Huntington predicted as far back as the 1980s, a struggle of “The West versus the rest.” No sentient being wants that war.

The best thing for Dubai Ports’s opponents to do at this point is to suppress impulse – political, emotional, or reptilian – and reconsider the deal. In policy, as in business, the rule is clear. Heed your lizard. But never let him dominate.

Miss Shlaes is a columnist for Bloomberg News.