Tribunals of inquiry are strange beasts. They occupy a no-man's-land between two separate branches of government. A tribunal is an arm of the Dail, but it is not part of the legislature. It has the powers and some of the procedures of the High Court, but it is not part of the judiciary. In theory it is a cold, fact-finding mission. In reality, it is a peculiar mixture of courtroom, theatre and gladiatorial arena.

It is not surprising that lawyers sometimes get confused and imagine that they are back in the familiar surroundings of the Four Courts. The result is something like the extraordinary confrontation at the Flood tribunal which ended with yesterday morning's climbdown by Garrett Cooney.

At the root of the affair was Mr Cooney's belief that Mr Justice Flood should force James Gogarty to act like a witness in a trial. In a court, the witness has to answer questions concisely and precisely. What Mr Cooney called "speeches from the dock" are not allowed. The balance of power lies with the cross-examining barrister, who can force the witness to give "Yes" and "No" answers which the witness might prefer to avoid.

Sometimes, when they have a very well-defined job to do, and when the basic facts they are exploring are not contested, tribunals can function with the ruthless efficiency of a court. Critics of the Flood tribunal point, for example, to the speed and clarity of the Finlay tribunal on the hepatitis C scandal or to the McCracken tribunal on Ben Dunne's payments to Charles Haughey.

But they forget that in each of those cases the basic story was known in advance, and the broad sequence of events was not in dispute. The Blood Transfusion Service Board did not try to claim women were not infected because of its negligence. Ben Dunne did not deny he had given large sums of money to Charles Haughey.

The Flood and Moriarty tribunals are not like that. They have open-ended mandates to investigate a huge range of potentially corrupt behaviour. Particularly in the case of the Flood tribunal, almost every detail of James Gogarty's evidence is contested by JMSE, Bovale and Ray Burke. The inquiry is, unfortunately for Mr Justice Flood, much more like the dreaded beef tribunal than the rightly praised McCracken investigation.

Many of the problems which reached a climax this week are rooted in the understandable horror of some of the main participants at finding themselves in this situation. They are reluctant to face the fact that while some of the excesses of this kind of tribunal are avoidable, many of them are not. Garrett Cooney wants James Gogarty to behave as if he were a witness at a criminal trial. (Indeed he sometimes gives the impression that he would prefer Mr Gogarty to behave as the defendant.) He seems to think that James Gogarty's rambling answers, counter-punching technique and refusal to treat his cross-examiner with due deference are entirely out of bounds.

If he had worked at the beef tribunal, he would know that they are in fact typical of this kind of proceeding. They come with the public, political and media-saturated territory that such tribunals occupy.

The truth is that people don't go to these kinds of tribunals merely to assist the judge with the clarification of facts. They go looking for vindication. They want to be proven right, not just in the eyes of the judge, but in the eyes of the public. They play to the gallery, both the immediate audience in the room and the wider gallery of the media. They score points. And, though they can to some extent be restrained, they cannot be controlled.

Often, the points they score have very little to do with the actual subject matter of the tribunal. The most spectacular example came at the beef tribunal when Albert Reynolds, then Taoiseach, effectively accused his own minister for industry and commerce, Des O'Malley, of perjury.

The subject - the precise size of Goodman International's claim for damages in a court action against the State - was of no real importance to the tribunal. And in any case Goodman's claim was not actually capable of being precisely quantified. Yet the dispute not only took up much of the tribunal's time, but spilled out into the political arena and brought down the government.

That incident demonstrated in the most dramatic way that there is not, and cannot be, a clear line between a public inquiry and the political process. The cross-examination of James Gogarty, whose allegations have already led to the departure of a senior minister, is not and cannot be a purely legalistic process.

Garrett Cooney's mistake was to try to insist that it could be and that he could practise his skills of cross-examination as if he were in the hermetically sealed atmosphere of a courtroom.

On the other hand, however, Mr Justice Flood fell into the same trap. It is perfectly understandable that he wants his tribunal to be conducted with efficiency and decorum. His desire for the tribunal to be a calm assessment of facts is laudably idealistic.

But he will have to get used to the fact that he is not acting as a judge in charge of his own court. He is acting in what is, essentially, a political capacity, as an arm and agent of the Dail.

He has the enormous burden of being judge, jury and high priest, upholding the law, deciding the facts and conducting a kind of ritual expiation of the sins of the body politic all at the same time.

He is at the centre of a conflict in which power, money, reputations and the political process itself are at stake. If he's going to walk out every time someone criticises him, to treat any expression of unhappiness as an insult to the judiciary, the tribunal will take a very long time to get through its vital work.

For the one certainty in what has been an extraordinary, unpredictable process is that there's going to be a lot more anguish and vituperation in Dublin Castle before the tribunal is over.

Whether he likes it or not, Mr Justice Flood is holding the ring for a fierce struggle over the future of Irish democracy. The chances are that the closer the tribunal gets to the truth, the more ferocious will be the emotions unleashed in front of Mr Justice Flood.

Hopefully, after the strange events of this week, he will have a clearer sense of what he's got himself into.