The prosecution's appeal against Anwar Ibrahim's acquittal in Sodomy II continues today with defence lawyer Ram Karpal resuming his submissions on the semen samples taken from complainant Mohd Saiful Bukhari Azlan.
Ram indicated to court yesterday that he would need another two hours to wrap up his submission. He is expected to provide further arguments on the issue of the integrity of the semen samples and the possibility of the samples being tampered with.
Much focus on the prosecution and defence rests on the integrity of the samples as Kuala Lumpur High Court judge Mohd Zabidin Mohd Diah in acquitting Anwar, found it was not safe to call for conviction based on the possibility that the samples could have been tampered with. 
It was revealed in court that investigating officer Supt Jude Blacious Pereira had opened the sealed plastic bag from Hospital Kuala Lumpur (HKL) and placed the 12 samples in separate envelopes before handing them over to the chemist for analysis.
While government appointed lawyer Muhammad Shafee Abdullah maintained the chain of evidence was not broken despite the plastic bag from HKL being opened, Ram suggested otherwise due to the “pristine” nature of the semen samples despite being examined four days after the alleged incident.
After the alleged sodomy incident on June 26, 2008 at the Desa Damansara condominium, Saiful testified that he did not bathe and wash in order "to keep the evidence". He lodged a police report two days later and the samples were retrieved on the night of June 28 and early morning 29.
The samples were then kept by Pereira, not in a freezer as instructed by HKL doctors, but in a metal cabinet in his office and later handed to the chemist on the evening of June 30.
Shafee (right) had also made a technical argument in that the court's test should be on the balance of probabilities, while senior counsel Karpal Singh said this was wrong as the court must adopt the ‘beyond reasonable doubt’ approach.
In criminal proceedings, the prosecution is often required to prove its case beyond resonable doubt while normally the balance of probabilities is adopted in civil cases.
After the defence submission this morning, Shafee will proceed with his reply. He took two and a half hours in arguing the prosecution's case yesterday.
It would be interesting to see whether the three-member bench led by justice Balia Yusof Wahi will deliver its decision today or instead announced it at another date.
For Anwar, the decision may affect his bid to contest in the Kajang by-election where nominations have been fixed on next Tuesday.
Malaysiakini is covering the second day of the Sodomy II appeal hearing LIVE.
LIVE REPORTS
12.30pm: As soon as Anwar exits the court he is greeted with supporters packed outside.
About 20 supporters encircle him shouting "Reformasi" loudly four times, while security in the area is tight. The hearing continues after Friday prayers.
12.22pm: Court breaks for Friday prayers and will resume at 2.45pm, with Shafee slated to submit. Shafee promises his submission will take half an hour.
12.12pm: Noorin says that degradation had been taken into account in the analysis.
She says the differential fraction examination process to separate the sperm and non-sperm cells were performed.
"The sperm fraction tests were done and the chemist said there was sperm already there."
She says that had Seah admitted there was contamination in the peri-anal region and the unknown contributor is the non-sperm.
The learned judge had actually dealt with the scientific evidence at the end of prosecution's case and Noorin claims that Justice Zabidin did not go through that evidence in defence.
12:05pm: Noorin says the word "pristine" came from McDonald as there is almost a high reading on the sample.
She defended that Seah had not said there was no degradation.
"Any scientist has yet to come up with a test on degradation as it will always be there, and it is a matter of interpretation."
"McDonald's last test was done in 2004, and since then, he only interprets the results," she says, pointing to McDonald's field work.
11.50am: Now DPP Noorin Badaruddin is submitting on the matter of the 18 allele.
"DNA profiling is based on the 16th DNA loci. The 18 allele is found on one or two locus to two different chemist.
"That is why Nor Aidora (the chemist) did not report the 18 allele. The allele is only found on one loci and it was not necessary to report it."
11.47am: Karpal replies to Shafee on the question of the alibi of the witness.
"By right, the statement made from the dock is evidence and it must be considered.
"This is also misdirection of the judge which requires attention (by this court)."
Karpal ends his submission.
11.42am: Anwar’s counsel Karpal Singh says Shafee suffers from “bouts of amnesia” as the Umno lawyer said that a person who testifies from the dock is of low-mental capacity.
"However, Shafee had represented DP Vijendran and he testified from the dock."
Justice Zawawi asked if this was in reference to the the former deputy speaker, to which Karpal replied yes, to laughter in the court.
He adds that statement from the dock is evidence.
11.40am: Ram says investigating officer Supt Jude Blacious Pereira had been found "a liar" in the past and the finding was made by Shafee.
"We find the evidence of Jude as totally unsatisfactory as he is constantly not telling the truth or suffer from absence of memory and that is what was written by Shafee," he said.
Jude, Ram said, is central to the exhibits.
"He had the sample and intimate samples. There are third-party allele in there.
"This is what we call tampering. We have to support the finding of the High Court judge as what if the swab used were tampered with."
Ram concludes his submission.
11.35am: Ram says the manual on this states that the separation of the cells must be made to remove non-sperm cells.
"The fact remains that in the sperm fraction analysed, there is non-sperm cells in them.
"It can be modified and even if the prosecution's version (is correct), it would be impossible to say that the sperm cells comes from male Y," he said.
Ram says Seah cannot say that for sure and as such, Shafee should not be saying that the sperm cells are from male Y (Anwar).
11:30am: Anwar's supporters have shifted to the back door to await the opposition leader when he is led out of court.
To while away the time, 'Uncle Sow' recited poetry to the listening group.
11.25am: Ram submits that Seah did not separate the sperm fraction and other cells.
"She says it is impossible to separate sperm and non-sperm cells. But our expert witness (Australian DNA specialist Dr Brian McDonald) says it is possible to separate them."
"When she says the sperm cells came from male Y (Anwar), she is merely assuming it came from sperm cells. However, the separation was not done," he said.
11.15am: Ram says the DNA tests were not properly carried out.
"It was not determined which cell source the DNA came from."
"DNA can come from skin, hair, saliva, sperm, etc. It is not in dispute that when it came to the chemist, it came in the form of mixture and there is doubt that the sperm is actually from male Y (Anwar)," he says.
11.12am: Court is in session.
11.10am: DAP parliamentary leader Lim Kit Siang enters the court. Also in court are other lawmakers, Johari Abdul, Wong Chen and Sim Tze Tzin.
10.57am: PKR director of strategy Rafizi Ramli is seen on the grounds, chatting with the gathered supporters.
Meanwhile, three police four-wheel drives is observed there, with the dogs from the K9 unit inside.
10.40am: Court recess.
Meanwhile outside, some 80 supporters of Anwar Ibrahim gather on the grounds next to the Palace of Justice.
According to one supporter who came from Penang, the group have gathered peacefully there as they were not allowed into the courthouse.
“They (the police) did not allow us entry, so we gather here. That is alright as there is shade beneath the tree. We come to support Anwar, that is all,” he says.
Meanwhile, three uniformed police personnel are seen in the area monitoring the group.
10.30am: Ram further defends the expertise of the foreign experts which Shafee had earlier questioned.
Ram says Shafee takes a simplistic view of the law in excluding all this.
He adds that the required burden of proof requires that the integrity of the samples is ensured.
"However, in this case it is not... There are many questions. If there is anomaly it should be taken in favour of the accused."
10.20am: Ram says Shafee took a simplistic view by saying Jude only cut open the HKL plastic bag but did not disturb the samples.
Despite this, he says there are the unexplained contaminations.
"There are two types of contamination, direct and indirect.
"The cases referred by Shafee shows there was nothing peculiar but in this case, even if it is said that Jude cut the plastic, there is no explanation on the degradation and contamination."
10.10am: Defence lawyer Ram argues the possibility of the 18 allele coming from investigating officer Jude Pereira could be there as he held the samples for a period of time.
"It is not for us to speculate, but for the defence to create reasonable doubt. It is incumbent on the prosecution to exclude the presence of the third party."
9.50am: Ram questions chemist Seah's testimony on the high rectal swab as at first she said it the 18 allele was important but later when asked further in her testimony, she said it was not important.
He also raises questions on another chemist Nor Aidura Saedon's testimony over her examination of the 'Good Morning' towel.
"She said the reason she did not report the 18 allele as it is below the threshold and it could be a 'starter'.
"I put it to her it was not a starter, and it did not follow her Chemistry Department guidelines and she agreed."
The point, Ram says, the 18 allele is there, but the chemist did not conduct further tests on it as it is from another male contributor.
"It shows there is contamination in the intimate sample and we do not know who the contributor is."
9.40am: Ram moves on to the issue of contamination.
He says the 'Good Morning' towel retrieved from Anwar's cell have an unidentified characteristic with the presence of an 18 allele in the DNA reading.
"The 18 allele, is also present in the high rectal swab. This means a third person's DNA has been found in the anus but high up the rectal."
There are two ways this could happen. With the sexual intercourse, the semen was ejaculated inside the anus.
"Complainant (Saiful) says he is not homosexual, so how can one explain the 18 allele in there.
"The chemist says the presence could have been as result of drop-in (contamination)."
9.30am: Ram says chemist Dr Seah Lay Hong had testified there was no evidence of degradation to the high rectal swab.
"The point here is the prosecution is in agreement of the defence that the sample was 'pristine'."
9.24am: Continuing from yesterday, Ram Karpal submits that the peri-anal sample shows sign of degradation but the high rectal swabs shows no sign of degradation.
"All these samples are taken at about the same time and all should show signs of degradation. However, the high rectal swab did not.
"This raises the question on the possibility of tampering."
9.14am: Court now in session with justices Balia Yusof Wahi, Aziah Ali and Mohd Zawawi Mohd Salleh on the Court of Appeal bench.
Balia complains that the proceeding is late by 15 minutes.
"When we say 9am, it is at 9am."
Defence lawyer Ram Karpal says they were on time and it was possibly because the court thought lead defence lawyer Karpal Singh will come.
"Karpal will come in later," he says.
Justice Balia wants the counsel to conduct the proceedings professionally.
Balia reminds them not to read from their submission as judges have already read them.
9.10am: The situation outside the court house is quiet and calm. There are about a dozen police officers milling around the area. There are no protesters today.
Meanwhile, there are about eight police officers standing guard at the back of the court complex. The police also brought in two dogs from their K9 unit.
8.56am: Opposition Leader Anwar Ibrahim and his wife, PKR president Dr Wan Azizah Wan Ismail, arrive at the Palace of Justice along with three of their children.
They go to the second floor where the Court of Appeal is located.
8.55am: Muhammad Shafee Abdullah, the private lawyer appointed by the government to lead the prosecution team in this appeal, enters the courtroom.
Also in court are a number of international observers as well as PKR supporters. The public gallery is filling up fast.
8.50am: Some embassies send two representatives, say court staff. Today there are more people asking for passes and some journalists may be - like yesterday - unable to go into the courtroom.
8.28am: Security at all entrances at the Palace of Justice in Putrajaya is tight, with uniformed police helping the court's auxiliary police.
[More to follow]