Public funded research in India because of its sheer size and proficiency holds key to India�s transformation to a knowledge economy in the near future riding on fundamental research and human resource generation. Subsequently, university system in India could refer to both the traditional university system along with the competently designed apex institutions (IITs). Alongside university research, a model of independent science research through dedicated institutions mainly through the CSIR network was designed to expedite the process of technological learning and catch-up.  However, science research in India reflects enormous heterogeneity in terms of quality. Overall, it is often contended that science research in India has not been quite so successful in generating the required critical mass of knowledge repository and manpower to adequately fuel the growth engine of the economy. We summarise some of the issues and areas of concern.
(i) Sub-optimum R&D Expenditure by international standards
Research and Development expenditure as percentage of GNP in 2005-06 stood at 0.89%. A quick international comparison reveals that developed countries on an average spends over 2% of their GDP on R&D, a cut above India�s spending. Even an emerging economy like China spends 1.42% of its GDP on R&D, again ahead of India. Only Brazil is somewhat close to India with 0.82% of GDP being spent on R&D. However, a sector wise break-up into shares of R&D expenditure in India shows that 74.1 % of the total R&D expenditure was incurred by the government and just 25.9% by the private sector during 2005-06.
(ii) Falling number of good faculty
It has generally been accepted that the number of quality entrants into the teaching and research profession has been reduced due to better remuneration elsewhere. Thus the real challenge is to attract good and competent candidates to the academic profession and also help them sustain their interest in teaching and research in the long run. It has been pointed out that government�s policy on promotions does not incentivise faculty to undertake quality research.
(iii) Poor quality of our PhDs
The quantity versus quality paradox of Indian higher education is relevant for research training also. Out of 18730 doctoral degrees awarded in India in 2005-06, 8420 (accounting for 44 percent) were from the sciences and 103105 (55 percent) from humanities. In sciences, 5625 doctoral degrees (accounting for 66 percent of total science PhDs) were awarded in pure scientific disciplines, 1058 (12.5 percent) in engineering and technology, 1119 (13.3 percent) in agriculture and 438 (5.2 percent) in medicine. While the numbers might appear impressive, there remains a big question mark about the quality of many of these PhD degrees.
(iv) Sub-optimum patenting and publication activity
Although patenting is still not very common among academic researchers in India, some of the S&T institutions, particularly the CSIR network, have put in place an institutional framework to encourage patenting of their research outputs. It may be noted that the number of US patents granted to CSIR jumped to 196 in 2005 from just 6 in 1990-91. Although, prima facie we observe a spurt in patenting activity from a handful of laboratories, very few of these patents have actually been licensed to the industry. Overall, India�s contribution in the world publications has increased marginally from 2.1% during the 1995-2000 to 2.3% during 2000-2005.  Although India’s impact factor (average number of citations per paper) is not yet at par with the world average within most scientific fields, it has made significant gains in Physics, with an average of 3.13 cites per paper for the period 2003 to 2007.
(v) Ambivalence towards IPR issues
Scientists in India have often been viewed as �lethargic� towards active participation in commercialization of their inventions. Dedicating research outputs to public domain for free use and follow-on research has been a standard practice. The National Knowledge Commission of India (NKC) constituted by the previous government came up with a strong recommendation for a new legal framework, mandating disclosure and patenting of output from public funded research along the lines of the US Bayh-Dole Act. However, in the absence of an appropriate understanding of the Indian context of academic research, this Act might affect the existing balance of incentive structures.
One might find it useful to concentrate on mitigating more fundamental problems affecting the Indian academia in the first place beyond IPR related concerns. Moreover, there is every need to systematically understand the complex matrix of incentives affecting the various tasks performed by a typical university faculty prior to any institutional and organizational reform. It also remains to be ascertained whether financial incentives alone can influence faculty performance. Justifiably, appropriate alignment of incentives is required to ensure quality in research and training as well as in boosting efforts toward commercialization of public-funded research.