For me, it's a balancing act. I have less faith in the actual methodology and funding processes of Science, and the way it ties into the growing Patent debacle. There is too much politicization and shading of results to fit a certain perception. There are too many studies on products or processes funded by the very companies that own those processes that are given equil weight to supposedly independant studies. Important studies are often under funded, not blind, lacking in adequate controlls, and performed by graduate students whose entire future employment and funding is based off having a flashy result that catches attention. The peer review process has failed. No one has time to attempt to reproduce studies unless they are earth shattering or potentially commercially viable, and even then, when there is time for people to attempt to reproduce them, you end up with situations like this. http://news.yahoo.com/cancer-science-many-discoveries-dont-hold-174216262.html
Science, supposedly the inviolate collection of things we "know" is based in many areas on a foundation of graduate student work that doesn't hold up under scrutney in some fields. Particularily in medical research and climate sciences. Physical research into things like aerodynamics and rail gun research tends to be somewhat easier to check, so seems to me to suffer less from this, though they have another problem where companies tend to snap up any research patents related to a specific area and sit on them, stifling real world applications to protect their own product line. And yes, I'm looking at you, battery industry as a whole...
To compound things, the various government agencies and research houses that should be providing a large portion of pure, unbiased research on a continueal basis are under assult. They were never completely apolitical, regardless of what the propaganda films of the 50's would have us believe, but its gotten much worse over the years. At the same time, budgets are shrinking, and colleagues find themselves forced to throw their comrades under the funding bus in order to secure their own projects. Couple that with shrinking saleries and benifits, and the truely "good" scientists are leaving public service in droves. The fact that it took an act of congress to get the Alpha magnetic spectrometer launched, we cancelled most of our mars missions, major climate science satilites remain unlaunched or crashed due to haveing to use cheaper, less sucessful launch alternatives is criminal.
Then we have people on all sides of issues who see no problem with lieing to further their own agenda. Are the majority of scientists dishonest? No. but it only takes a few vocal bad apples to spoil public perception. When you have 4 people talking about the same issue, each with incontrovertable proof that directly contradicts the other 3 people, someone sure as **** isn't playing fair.
I feel that the scientific method is sound. If employed properly, given enough time, and given adequate funding with an enforced level of consistancy, independance from funding sources, and adequate peer review, then science can prevail. I feel that in the current climate, a significant portion of our basic foundation research in many fields is potentially suspect. I feel the problem will get worse with time unless something is done, and I feel that the media bears an equil portion of blame in all this for sensationalizing everything they think can result in a story and not listening to evidence.
Take climate change for example. I'm a conservtive and a republican for the most part, and I believe that there is climate change, and that humans are responsable for a portion of that. I also however definitly disagree with the causes, scope, and projected timeframe for occurances. If nothing else, our understanding of how Sol and our radiation and magnetic belts interact with our atmosphere and any related heating or cooling affects is almost non existant at this time. We also don't have any kind of satilite that can accuratly measure ground temperatures consistantly and compensate for moist adiabatic lapse rate atmospheric contraction variations enough to make projections where +/- 1 degree variance has a significant effect on the outcome. What is fine for weather forcasting day to day is problematic in reconciling satilite data with ground measurements. Historical ground measurements are also problematic, given variances in equipement(particularily the recording methods), dispirate sources recording the information(some with agendas), and spotty overal coverage in some areas. They also tend to ignore or underestimate the effect of ground soak energy caused by cutting down all the trees in an area and paving everything in sight. replace 50 miles of trees with 50 miles of black tar asphalt? sure of course the weather patterns in the area are going to change. is it due to CO2 emissions? possibly not.
Thats just one aspect of science where I think that anyone who can claim "we know and understand this phenomenon well enough to make massive, sweeping environmental changes with profound economical impacts, or well enough to say at this point we can safely ignore this" is an idiot. In the 1970's we thought we were about to enter an ice age. In another 20 years, we'll probably decide that alien death rays are trying to microwave us. The point is, we don't know, and it could be somethign serious enough that we should devote a much larger research budget to the issue, at the same time striving to ensure that money is used independantly for pure climate research, but not make sweeping economically stifling changes on a "hunch".
The patent office needs to be redone as well. if you invent something, you should be compensated, but there needs to be a mechanism to encourage innovation too. Weaponization of patents in the form of patent troll lawsuits is why we don't have evryday use jetpacks yet, and you should all be ****** about that.