The prosecution's appeal against Opposition Leader Anwar Ibrahim's acquittal of Sodomy II will finally be heard at the Court of Appeal. The court has set aside two days to hear the appeal - today and tomorrow.

This comes after the Federal Court yesterday dismissed Anwar's last-minute bid for a stay of proceedings following his failure to remove top lawyer Muhammad Shafee Abdullah from leading the prosecution team.

This was Anwar's third attempt to remove Shafee - this time on the grounds that the Umno-linked lawyer was an “unfit and proper person” to lead the prosecution and for alleged conflict of interest.

The Court of Appeal however rejected Anwar's application, arguing that Shafee's name was not struck off the lawyer rolls.

The appellate court in not allowing for a stay of that decision pending appeal to the Federal Court, also ruled the application was vexatious and an abuse of the court process.

The first two applications to remove Shafee was made last year on the grounds his appointment via a fiat granted by attorney-general Abdul Gani Patail was not proper under the Criminal Procedure Code.

The second is based on former Kuala Lumpur Criminal Investigation Department chief Mat Zain Ibrahim's statutory declaration over his meeting with the controversial lawyer and the ex-top cop’s personal knowledge of Abdul Gani's alleged misconduct in Anwar’s black-eye incident.

In a rare move, Abdul Gani appointed Shafee last July to lead the prosecution and the appeal has been pending since.

In addition, Anwar's defence team that comprises senior lawyer Karpal Singh had also applied to recall the investigating officer Supt Jude Blacious Pereira to testify at the Court of Appeal but failed when the Federal Court allowed Shafee's preliminary objection to strike out the appeal.

The appeal on that application was heard without Karpal being able to file the petition for appeal, which was supposed to be due today.

Against this backdrop, the prosecution's appeal will be heard led by a determined Shafee and lawyers from his firm, as well as Attorney-General’s Chambers deputy public prosecutors, Noorin Badaruddin and Mohd Hanafiah Zakaria, who were retained from the last prosecution team.

Anwar was acquitted by the Kuala Lumpur High Court judge Mohd Zabidin Mohd Diah on Jan 9, 2012, of sodomising his former aide Mohd Saiful Bukhari Azlan, in 2008.

The hearing is expected to attract international observers from Lawasia, Internatioal Parliamentary Union, International Federation of Human Rights and International Council of Jurists.

Malaysiakini is covering the court hearing LIVE.

LIVE REPORTS

5.36pm: Ram Karpal says it was important for the court to note that it was 96 hours when it was not preserved. 

5.15pm: Ram says the samples should have been placed in a freezer at minus 20 degrees.

"Both witnesses, local and foreign chemists, agree there will be degradation (of DNA samples) and it could be stopped by placing it in a freezer.

“As degradation gets worse, you start losing samples to make copies, resulting in unreliable DNA,” he says.

5.11pm: Court back in session.

4.55pm: Court takes a 15-minute recess.

4.35pm: Ram says the DNA samples retrieved were found to be in pristine condition, considering it was 96-hours-old when examination was carried out by chemist.

"One can recognise degradation from the DNA graph. Degradation is expected to happen and it (DNA samples) reached the chemist after four days.

"However, Dr Seah said degradation is if no concern to her. The prosecution is in agreement that there is a high degree of the effects of degradation.

"Degradation is due to bacterial growth as a result the samples not being preserved, as a result of it not being placed in a freezer."

“One would expect there will be degradation, (so) how is it that there were no degradation after the samples were only given to the chemist four days after the incident,” he says.

Hence, Ram tells the court that those samples could not have been the ones retrieved from Saiful. “It is possibly not the same samples taken."

4.25pm: Ram Karpal says the 'Good Morning' towel retrieved from Anwar's lock up was also contaminated.

He adds that the items were illegally obtained and inadmissable.

"If this is taken into consideration, there would not be a 'Male Y' and the entire prosecution case falls and Anwar's defence would not be called."

4.10pm: Ram Karpal says the judge was wrong to call for defence as there is no prima facie case.

"There was contamination in the peri anal swab, and also on the lower rectum swab. This is not disputed. There was another male contributor. There is a mixture of semen containing Saiful's DNA, ‘Male Y’ and there was another male contributor retrieved from the peri anal area.

"There is a third male contributor for the rectal swab perhaps the complainant had been penetrated by another person or third party."

3.40pm: Karpal reading Saiful's testimony, saying he is not a "country bumpkin", as he has got tertiary education.

"Saiful said he was afraid of Anwar but he could have left the place. The door was not locked, he could have escaped. He attended a function the next day. It was obvious he lied when he said the incident took place 'tanpa kerelaan' (without consent)

"Saiful delayed in making a report two days after incident. He did not go to HKL first but went to another hospital."

3.55pm: Karpal says Saiful met many people but did not actually report the matter directly.

He noted that Saiful ( left ) met (former Anwar aide) Ezam Md Noor and also Mumtaz Jaafar (a friend of Prime Minister Najib Abdul Razak’s wife, Rosmah Mansor) but did not lodge a report then.

Dr Mohd Osman Abdul Hamid, the Hospital Pusrawi doctor, Karpal says should have been called by the prosecution when Saiful told the doctor that he was assaulted with a plastic object that was inserted in his anus.

"It was not a conduct of someone who has been ravaged."

He says the defence was “not a bare denial” as “we called two experts”.

3.35pm: Based on what had been said, Karpal argues that Anwar should not be called for defence in the first place.

"The court must subject maximum evaluation, and the court should consider Saiful's evidence with care as it did with Azizan Abu Bakar (in Anwar’s first sodomy case), which was described by the trial judge to be a credible witness as strong as the Rock of Gibraltar, but the Federal Court overturned this."

3.25pm: Karpal submits on the uncertainty of the samples being compromised.

The trial judge, he adds, was correct in acquitting Anwar as there were questions regarding the integrity of the samples.

"It is wrong to say that the judge did not take into consideration the defence witnesses Dr David Wells and Dr Brian McDonald. There was a latent defect in the prosecution's case.”

"The sample was taken 56 to58 hours after the incident. The sample was not placed in a freezer but it was found in pristine condition despite the threat of degradation from bacteria."

3.00pm: Karpal says Jude, as the star witness, testified that degradation may take place.

"Dr Siew asked Jude to put the samples in a freezer but he did not do so and this shows the sample was compromised when he placed it in his cabinet."

"The cabinet is not a freezer, and when asked by Sankara Nair if this is not against police procedure, Jude did not answer that question. He knew he should place it in the freezer to prevent degradation. This shows Jude did not follow Dr Siew's direction and this shows he went against the IGSO.”

Ram Karpal says the samples were given on early June 29 and he cut it open that same morning. Ram adds that Jude only gave the samples in the late evening of June 30.

Karpal says Shafee is maligning Anwar and should apologise.

2.50pm: Karpal says that every extent of a criminal case must be proven beyond reasonable doubt.

Shafee, Karpal adds, is talking about the evidence of Jude when he had condemned the same witness in the Suhakam inquiry.

"He also brought to court and contends the bottle contains the samples which had been given to Jude, given by Dr Siew."

2.40pm: Court resumes.

Karpal submits that the court must follow the evidence adduced. He takes strong objection to Shafee's remarks on Anwar.

"An accused person need not put up defence, he can remain silent, make a statement from the dock or witness stand.

"Anwar chose to make a statement from the dock and the prosecution should not poison the minds of the judiciary by making such statements."

Karpal asked whether the standard of proof is balance of probabilities in a criminal case.

2.15pm: The courtroom is already packed. Counsel Karpal Singh will shortly submit for Anwar's defence.

12:40pm: Shafee says there was no conspiracy between Jude and the chemist. "Where will Jude get the accused's sperm?" he asks.

Justice Aziah asks if the trial judge addressed that and Shafee replies, "How could Anwar's sperm be 4cm in Saiful's anus?"

"The judge did handle this in his judgment (but despite this it resulted in an acquittal)."

"Not only must have Jude obtained the semen but he must have obtained a degradation sample, in order to to prove conspiracy. Judges must watch National Geographic and all."

To the laughter of the gallery, Justice Aziah responded, "We watch CSI."

Shafee says the appeal must be allowed as the evidence is overwhelming and this is one case where the court cannot resist to do so.

Court in recess. Hearing will resume at 2.30pm.

12.25pm: Shafee shows Anwar's notice of alibi and that at the time the opposition leader was not at the Desa Damansara condominium unit where the alleged incident took place.

What Anwar stated in the notice is that he was in the next door unit and this was a devious manouevre, adds the lawyer.

"There are 14 witnesses, they say, but none were called to support the notice of alibi."

12.15pm: Shafee ( right ) says the pictures and video recording at the scene proved Anwar was there.

"Not a whisper of an alibi was produced. The defence is dishonest when confronted with the video, they dropped the entire defence without a whisper."

12.05pm: Court now asks whether the trial judge accepted Anwar's statement from the dock.

Shafee, in describing the High Court judgment, says it is like reading an Agatha Christie thriller. It is only in the final two points, the judge decides to acquit.

"The judge is for the prosecution all the way but in defence he was about 90 per cent for the prosecution. It is only in the final two points, he decided otherwise.”

Shafee says the judge never took into account of the accused’s statement from the dock.

"It was a mere denial (statement from the dock) and it is a classic bare denial. A denial of this sort after he gave a notice of alibi. He (Anwar) said he was never there but no witnesses are called to support the alibi."

11.55am: Shafee contrasts this case with another case where three test tubes were not sealed but the court accepted the evidence as there was no broken chain of evidence.

"In this (Anwar’s) case, the chemist received the samples sealed, yet this resulted in an acquittal."

11.45am: Shafee says the trial judge made the mistake when he misconstrued that the individual bottles containing the samples were tampered with.

Actually, it is only the plastic bag which defence witness David Wells agreed had been tampered with, he adds.

"However, when asked by (former solicitor-general II Mohd) Yusof ( Zainal Abiden) the witness said he remains uncertain if the integrity of the samples were compromised.”

Shafee points out that in a criminal case, one should argue on balance of probabilities.

He adds that the IO followed the IGSO under scientific assistance, where all items should be packed differently and not mixed together and labelled clearly.

In this case, HKL doctors placed all the samples in a plastic bag.

11.30am: Court in session.

Shafee says Anwar's foreign expert Dr David Wells said that the plastic bag in which the samples were placed were not tamper proof.

The appointed lawyer argues that in Australia they may not extract samples after 36 hours but that is not gold standard.

11am: Justice Balia remarks that all evidence are sealed. Shafee further submits that the seals have the doctor's and Saiful's signatures on them.

"This is an added precaution... As normally the doctor's signature is sufficient," he said.

Court takes a 15-minute break.

10.50am: Shafee says if the chemist took all the precaution from the hospital and the IO, how could the judge ignore this.

There is silence in the gallery.

The appointed DPP says the Borang Pengendalian (handling form) revealed that the samples were sealed by Dr Siew.

"It is difficult to say the doctors and IO conspired. I would say the IO's evidence is impeacheable."

10.46am: Shafee shows judges the HKL plastic bag used to keep the samples, that was cut open by Jude."It was cut open with the bottom portion still dangling."

But all the samples are placed in separate envelopes according to the IGSO as explained earlier.

The chemist, Shafee says, did not reject any of the samples given by Jude despite this.

10.40am: Chemist Dr Seah Lay Hong testifies that the seals on the samples taken at Hospital Kuala Lumpur remained intact."The security label placed remained intact. The seals remained intact."

10.30am: A man attracts the attention of Anwar’s supporters outside the court with his anti-government songs and poetry, including criticising former prime minister Dr Mahathir Mohamad.

He says he is from Penang and now lives in Kuala Lumpur, and has been at the Palace of Justice since 8am. However, he declined to disclose his name.

Another Anwar supporter claims that the man is "Uncle Sow", and has been a loyal attendee at court every time Anwar is tried.

10.30am: Shafee says there is no evidence of tampering as the seal on the recepticles remained intact despite being placed in envelopes.

10.25am: Shafee says the investigating officer placed the bottles in separate envelopes. "The exhibit inside remains intact and the seal remains intact."

He adds that the judge made the mistake in deciding that the plastic bag with the samples sealed were torn amounting to tampering.

"I suspect he (the trial judge) must have confused it with the bottles that were sealed."

10.13am: Shafee says the samples retrieved from Saiful's rectum was in "pristine" condition despite it being retrieved 56 hours after the alleged incident.

He says the trial judge took the easy way out, when they accepted the foreign experts' testimony. He claims these these experts relied on textbooks as compared to the local chemist, Dr Seah Lay Hong, who is a specialist in her field and has done extensive field work.

"The learned judge misconstrued the facts. There were several bottles sealed and put in a plastic bottle. The doctors did not mark any numbers they write upper rectum, low rectum and peri-anal."

The bottles were all sealed and signed by the doctors and counter signed by Saiful.

Shafee says the samples were placed in a plastic bag.

However, the investigating officer (Jude) said according to the IGSO (Inspector General Standing Orders), the samples had to be separated and not all placed in one plastic bag.

10.10am: According to Shafee, sometimes you cannot find injury to the anus when a lubricant is used (the KY jel).

He says from the fingernails of Saiful, there were skin traces of the accused.

10.08am: Shafee says there is no explanation how the accused (Anwar's) sperm was in Saiful's anus.

"With the conclusive finding of the discovery of the sperm, the doctors concluded there was penile penetration."

10.05am: Shafee says the collecting of samples was done by the three Hospital Kuala Lumpur doctors and according to them, there is penetration in Saiful's high and low rectum.

Lembah Pantai MP and Anwar's eldest daughter Nurul Izzah and her husband are also in court but both are standing at the back.

9.55am: In term of reasonable doubt, Shafee says there is no need to create 100 percent reasonable doubt.

He refers to Section 3 of the Evidence Act, what needs to be proved is a fact of issue is a balance of probabilities and not 100 percent.

"It is a probability test. How do we prove a case beyond reasonable doubt, all facts must be gathered and the cumulative facts to prove the case."

"The judge imposed a high burden that the integrity of the sample is compromised. That generated the acquittal by raising the doubt," he says.

9.45am: According to Shafee, the foreign chemist hired by Anwar had created doubts to the integrity of the samples.

This is despite the judge earlier had ruled in accepting the testimonies by the prosecution witnesses resulting in Anwar's defence being called.

"However, there is nothing in the written judgment to say the court was convinced by the foreign experts."

"The judge only says there is no 100 percent certainty that the samples remained intact," says Shafee.

9.45am: Shafee says there is a mistake on the part of the trial judge to question the integrity of the samples from Saiful's rectum.

He adds the trial judge also made a mistake in questioning the chemist report and the DNA findings.

The chemist, he says, had taken into consideration of all factors.

"There is no evidence of the samples from the rectum were tampered as the seal is intact," argues Shafee.

"The judge also failed to take into consideration of corroborative evidence."

9.40am: Shafee says there is one single issue that results in the acquittal of Anwar, namely the DNA exhibits recovered from Saiful's rectum was compromised.

He says the question is whether there was tampering by investigating officer Jude Pereira, the integrity of the samples that were preserved by the two chemists and whether their testimony could be relied upon.

Shafee said the petition of appeal is focused on this.

9.35am: Shafee introduces all the parties involved in the case. Also present is complainant Mohd Saiful Bukhari Azlan's counsel Zamri Idrus.

Shafee says the prosecution's submission had been tendered on July 19 .

Seats inside the courtroom are all occupied with many more unable to get in waiting outside.

9.30am: Court is now in session with justice Balia Yusof Wahi leading the three-member Court of Appeal panel.

9.29am: Unlike yesterday, the situation outside the Palace of Justice appears quiet. There is a small group of Anwar supporters under the watchful eyes of a dozen of police officers.

9.28am: Also in the courtroom are Kelana Jaya MP Wong Chen and Wangsa Maju MP Dr Tan Kee Kwong. Outside is another opposition representative, Seri Setia assemblyperson Nik Nazmi Nik Ahmad.

9.21am: Pandan MP Rafizi Ramli and a dozen of supporters from the Malaysian Indian Force and PKR Youth are blocked from entering the court house.

However, only Rafizi is allowed into the courtroom.

9.20am: Shafee Abdullah's prosecution team is already in court. Now awaiting for defence lawyer Karpal Singh.

9.19am: The court room is packed to the brim.

International observers from Lawasia, International Commission of Jurists and Inter Parliamentary Union's representative Mark Trowell are among those in the public gallery.

9.10am: Anwar Ibrahim and his wife, PKR president Dr Wan Azizah Wan Ismail, arrive at the court house. They are accompanied by two of their daughters.

They go directly the Court of Appeal on the second floor of the Palace of Justice.

9.05am: Following yesterday's incident where a crowd of Muslim NGOs attempted to storm the court house, security has been tightened at the Palace of Justice.

People are not allowed to enter the back entrance and must use only the front entrance despite both the back and front sections are equipped with X-ray scanning machines.

The Court of Appeal panel will be chaired by justice Balia Yusof Wahi. The others are justices Aziah Ali and Mohd Zawawi Salleh.

8.53am: Security is very tight as police set up roadblocks near the back entrance of Palace of Justice in Putrajaya where the case will heard.