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The decision to play Imran Khan ahead of Abbas has attracted widespread criticism and surprise, which only grew as the Australians churned out a first innings of 580 in Brisbane with big centuries to David Warner and Marnus Labuschagne.
Waqar, Pakistan's bowling coach, explained that Abbas was still on a long road back from the shoulder injury that he suffered against New Zealand last year, subsequently being recalled somewhat hastily against South Africa and then playing for Leicestershire in the English County Championship.
Waqar indicated that Abbas' return to rhythm would hopefully occur in time for him to play with a pink ball under lights at the Adelaide Oval, in what now looks likely to be a match Pakistan must win to square the series.
"Mohammad Abbas has been a match winner for us over the last 18 months, he's been bowling really well," Waqar said. "Unfortunately he's not at his best rhythm and recently back in the New Zealand tour he had an injury so he wasn't bowling as good as he has done in the past against Australia and of course in England. But we're not losing hope in him, he's our main man and we're going to have a really close look and hopefully once we get into Adelaide we'll think about it."
Pakistan have insisted from the moment Abbas was dropped that he is not injured. This is now likely to invite scrutiny on how Abbas has been managed since that injury, which forced him to miss the last Test against New Zealand in Abu Dhabi and the first Test in South Africa. Since then he has played two Tests in South Africa, three ODIs against Australia in March, a substantial portion of the county season, and three games in the Quaid-e-Azam trophy as well.
"It's a decision that depends on the head coach and the selectors on who'll play and who won't," Waqar said. "But it would be injustice against Imran Khan to say that his selection was unjustified. His performance in first-class cricket has been great and so too in the warm-up game in Perth. He was bowling well. But unfortunately he couldn't do the same here."
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Looking at how the bowling attack had fared, struggling to find the consistency required to trouble Australian players hardened by plenty of Test cricket this year and far more familiar with the Gabba conditions, Waqar said that the youth of Naseem Shah (16) and Shaheen Afridi (19) needed to be considered.
"You can learn from your opposition always. Naseem is only 16 don't forget. Even Shaheen Shah is a teenager. Of course they're going to learn a lot from this tour, going further into their careers," Waqar said. "I'm very hopeful that these guys and the likes of Muhammad Musa and Mohammad Hasnain. They are the future of Pakistan cricket. All we need is time. We all need to give them time and hope that they learn in the next year or so and they'll be a force.
"It's difficult to say what was going wrong out there. We sit down every evening and we talk about it and try to teach them what lengths need to be bowled. I think we missed it. It was very obvious and everyone has seen that our lengths weren't right. With the first new-ball we bowled poorly. If we would have put the ball in the right areas, things might have been different. We got carried away and with a young attack it can happen in Australia.
"We have to be very careful with Naseem Shah. He's very, very young and we have to manage him well because he bowls very quick. You don't want to put too much load on him, be careful with him. He is the future for Pakistan. We have to use him sensibly and I thought that's what the captain did. He's a wicket-taker. It was just his first Test match."
Yasir Shah's selection, meanwhile, was put down to the fact that this was otherwise an inexperienced bowling attack, rather than the wrist spinner's handsome record of dismissing Steven Smith six times in Tests - now seven after his full-length drifter snuck under the Australian No. 4's bat.
"We thought of both plans [four quicks or three and a spinner]. But picking him had nothing to do with the fact that Yasir has dismissed Steve Smith six times," Waqar said. "Yasir is a match-winner and has won a lot of games for Pakistan. His track-record in Australia isn't great. But he has a lot of experience and we all thought he'll perform better but unfortunately that didn't happen.
"There is a lot of inexperience in the bowling and Australia is a tough place to bowl. Hopefully these guys are learning, and they are the future. One of them is making a debut, the other has played three Tests and one is making a comeback. It's not easy. But we are working on it and hopefully we will get better."