The problem was not with the research. There was some good work being presented. I won't be able to comment in detail, because I am as of yet not too familiar with the field and the work being presented was mostly experimental with a lot of jargon incomprehensible to me. Yet I could say that the quality was better than some of us would have expected.
The problem for me was with the presentation. Only two presenters were able to give a good a presentation, Dr. Sabieh Anwar and Dr. Abu Bakr Muhammad. This might seem like institutional bias. It really is not. There were clear differences in presentations. On one side were people presenting their work, and on the other a pair who was trying to make their work comprehensible to the audience, many of whom were not deeply into the field.
As proof of my being not institutionally biased I will say this out. Dr. Abu Bakr only made a good presentation. He did not talk about anything deep or very exciting. His talk was really the review of a few papers, very accessible and comprehensible to me when I looked at them later. He did not make any deep points, and though this talk was illuminating to me, I doubt it was so much for the real scientists present.
The other thing I noticed was something that has been talked about elsewhere. The conference started off with approximately over an hour of introductory speeches from various administrative members and organizers of the conference who had little to be talk of besides the accomplishments of each other. It was an elaborate set up where everyone got praised by someone or the other.
There was one good thing to remember. Dr. Sabieh and Dr. Abu Bakr made requests multiple times during the conference that the academic community needs to join hands together against the government's idea of dissolving the HEC. By the end, they managed to convince the organizing community of the their views and a resolution was quickly drafted and signed by all present.
It was an interesting conference, giving me faith that more can happen for Pakistan's scientific community, that it can grow to something that can make real and substantial contributions to human knowledge. I have hope.