The Central Criminal Court has heard the case against Patrick Quirke was based on a theory and not any hard evidence.

The jury has begun hearing the closing argument from the defence in the trial of the 50-year-old farmer who is accused of murdering his love rival Bobby Ryan.

Mr Quirke has pleaded not guilty to murdering 52-year-old Mr Ryan, who was a part time DJ, known as "Mr Moonlight".

Mr Ryan disappeared on 3 June, 2011. His body was discovered by Mr Quirke in a tank on the farm he was leasing from his former girlfriend, Mary Lowry on 30 April, 2013.

The prosecution alleges that Mr Quirke murdered Mr Ryan because he wanted to rekindle his relationship with Ms Lowry with whom he had been having an affair and that he staged the discovery of the body because his lease on the farm was coming to an end.

Senior Counsel Bernard Condon told the court that circumstantial evidence was not a shortcut to a conviction. He said the jury could not take a short cut around the "red lights of reasonable doubt" or elbow them off the pitch because they did not suit a tapestry of propositions made and delivered "with gusto" by the prosecution.

He said the jury must approach its function as scientists in a cold and dispassionate way and with the greatest skill available to them - skepticism.

He told the jury members they could not come back in six months and ask if they made the right decision, there was no second chance and this was "too serious" and profound.

He said they must begin their analysis of each of the propositions put forward by the prosecution by saying Mr Quirke was innocent and ensure the prosecution had proved otherwise.

He characterised the process as taking a journey in something forensically equivalent to a train.

"You are being invited by the prosecution to go to the last station on the line, it will be uphill and will twist and curve, there will be branch lines off it and the prosecution should be able to bring you to the very last station on the journey and the only thing they have is evidence - that is the fuel - and if it isn't the sort of evidence that you yourself would be happy to be convicted on, if it is not grade A fuel you will not get to the station at the top marked guilty." he said.

He said Mr Quirke was parked in the train station marked innocence and it was up to the prosecution to move him out of it and they had to do that with fuel which was evidence and this is where there was a big problem because the evidence was thin.

"You will have to pass through several stops, you may go past suspicion station, likelihood station and even probability station but if you get out there you are in the wrong place for conviction," he said.

He said it was not enough to do a person for murder on what is presented here which was in the realm of speculation.

"What is the evidence, the actual evidence not the speculation, not the nod and wink, not the 'give a dog a bad name’?

Mr Condon said he made no apology for requiring the jury to do this and said the jury did not get to take a short cut because the public are watching or because they had been here so long and they had to return a guilty verdict and approve of the gardaí and all the money put into it.

He said they could not approach the case in a less than proper way.

The defence was there to test the evidence and were entitled to do so, he said.

"When we shook this tree we got most worrying answers."

He said the investigation was sub-optimal and forensically barren and at least merited the jury to stop and look at it.

He said there was not one whit of evidence to support a suggestion by the prosecution that Bobby Ryan might have been lured into an old milking parlour.

Pathology evidence said there would have been blood but none was found. There was no explanation for this.

"When were the clothes taken off? Where? How? By Whom? Where is the phone? Who turned it off, how was it disposed of?? Who was in the van that left Fawnagowan, where was the body? Was it hidden in the van?"

He said throughout that area of the case which was the central area, there was nothing.

"If you are being invited to draw an inference you ought to know the primary establishing fact against which you are drawing the inference," he said.

If there were two options available the jury must choose the one consistent with innocence, he added.

Beyond a reasonable doubt was the "top level of proof" and was the most exacting standard.

He said a large part of the prosecution's case was based on the evidence of Mary Lowry and many of the allegations she "threw across the courtroom" at Patrick Quirke would not last five minutes if made on their own in a court.

The extent to which the case had been run on "Mary and Pat's broken relationship" had cloaked the paucity of evidence.

Mary Lowry had engaged in "striking revisionism" and was a witness of high unreliability, he said. 

He said she had "self reported" as being vulnerable when she had shown herself to be well able to stand up for herself.

Gardaí had adopted wholeheartedly propositions made by her in their questioning of Pat Quirke and the jury must not allow itself to be dictated to or influenced by the views of the gardaí.

He said garda questions in interviews with Pat Quirke were not evidence.

A lot of what was being presented in the case was the breakdown of a relationship, he said.

The closing argument from the defence will continue on Monday.

Earlier, in concluding his closing argument, prosecuting counsel Michael Bowman said it was the combined effect of the circumstantial evidence which was important and the jury was entitled to draw inferences.

Not to find Mr Quirke guilty would be an affront to common sense, he said.

The facts clearly communicated motive, opportunity and a state of knowledge of the accused man, he said.

He asked what were the chances that the man who was dependent on Mary Lowry financially and emotionally and was under significant financial pressure would have items seized from his home including evidence of internet searches on decomposition and discovers the remains of Mr Ryan in an area to which he had unrestricted access.

He said there was no other rational hypothesis consistent with innocence.

There was no doubt and no room for coincidence for what had taken place and the only verdict was one of guilty, he said.