The relationship between biotech or pharmaceutical companies and physicians is tenuous and ought to be so. The two groups are driven by divergent motives, and this is a barrier to cooperation. The doctor's obligation is to the patient's health. On the other hand, industry is (and perhaps rightly so) driven by financial incentive. They want to make a profit. This often coincides with helping the patient (after all, it's easier to sell an effective product), but not always. And herein lies the rub.
There have been many studies demonstrating the often subconscious effect of industry on physicians. Indeed, getting small gifts like pens and pads of paper have a remarkable effect on a doctor's prescribing habits even though the doctor does not realize this. In the past, biotech and big pharma had even more overt influences, offering all-expenses-paid "educational" vacations (1 hour lecture, 23 hours on the beach) or dinners at fancy restaurants in return for recruiting patients for studies. This had a detrimental effect on the objectivity of medicine and the care of the patient.
Furthermore, academic medicine and industry have to be divorced. Studies cannot be run by those with a financial (or other) conflict of interest. Studies are supposed to be objective and set the standards of care across the board; the amount of influence these journals have on medical decisions is staggering. It would be completely unethical for conflict of interests to taint such publications.
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