Sweetened Beverage Consumption, Incident Coronary Heart Disease and Biomarkers of Risk in Men
Koning,L. Malik, V., Kellogg, M., Rimm, E., Willett, W.,  Hu, F. Circulation. 2012

The above named scientists reviewed two very big longitudinal studies.  The people involved in the studies were men (health care professionals) and women (nurses).  The people joined the study several decades ago.  They answered questions about their health and diet and had lab work completed.  As the years passed, they continued to give information on their diet and lifestyle, diseases that they contracted (confirmed by records) and more blood samples at certain times.  This is the kind of study that is helpful in establishing links between what people do - or what they are exposed to - and disease occurrence. 

A person is interviewed and measured (weight, blood pressure, insulin test, etc) at the start.  This is their baseline.  They do not have any indication of heart disease or lung problems (if they do, they are not included in the study, for instance).  Every year or so they tell about their diet and behavior and when a disease does present itself, the scientists can associate that disease with something that happened in between.  This is not a randomized controlled experiment - which is the only kind of study that can really show cause.  It is however, a very good study and when you have thousands of people instead of ten or twenty the links from lifestyle to disease appear much stronger.  Even then, the link is found in a big sample of people and applies to big samples of people - it is not individual risk.
In this study, the scientists found that sugar sweetened beverages, (soda, juices and such, but mostly soda) were associated a higher risk of heart disease.  The important part is that they know why..  Just as being overweight doesn't cause heart disease directly, drinking soda doesn't lead straight to a heart attack.  If scientists can find the in between factor, the mechanics, and they make biological sense -it contributes to the "evidence".  

Here they found that the SSB consumption did change biomarkers or under the skin conditions that are themselves associated with heart disease.  People who drank several sodas a day compared to those who drank none, had higher triglycerides, lower HDL, more inflammation (CRP, inter luekin 6, TNf) and their leptin (appetite suppression) hormone was less effective.  The researchers expect that process is being triggered by the fructose.  Those who drank the most soda had about 20% higher risk of heart disease. 

The people in the study, again, were health care professionals.  They did not drink that much soda to begin with and may not be representative of the larger US population.  However, there is every reason to believe that drinking a lot of soda is not good for people. (it is important to note that in data analysis, there are procedures that allow us to pretend that everyone was the same weight and ate the same way - so that the impact on these biomarkers could be attributed to the soda and not some other part of the persons life)

The best part of the article is this statement - for my personal reasons: From p 14 in the above referenced study - 
Our results highlight the need for cautious interpretation of studies reporting positive associations between diet drinks and cardiometabolic and cardiovascular outcomes.
What that means is that they do not at this time support the hypothesis or suggestion that diet drinks cause the same problems as regular soda.  Yeah me! (cardiometabolic - think heart - so blood pressure, cholesterol, blood fats, inflammation - and metabolic - digestion and enzymes - insulin resistance, appetite control)