There has been a lot of press very recently about a new Java exploit. This is becoming a common occurrence for Java over the last couple years. However, there is some misunderstanding, especially in the media, as to how those vulnerabilities affect the average user. Many news sites even provide instructions for uninstalling or disabling Java on your computer, which is an overreaction.
Java is an operating system level programming language, just like the native C++ programming language on Windows and the native Objective-C programming language on Mac OS X. These programming languages have the ability to connect to the internet, to access the file system, and execute other functionality that is necessary to create programs. The unique thing about Java, is that it can be used in web pages, through Java applets. This is where the security issues lie. A compromised web page can execute malicious code on your computer through Java applets, and therefore, Java applets should be disabled on your system immediately. However, uninstalling Java on your computer is an overreaction, as many of your applications, including ChemDoodle, rely on Java and are perfectly safe to use. A hacker can just as easily write a virus in a native programming language, like C++ or Objective-C, and fool you into executing it on your computer to compromise your security, Java is not unique in this aspect. So if you are worried about desktop applications, don’t just uninstall Java, you might as well just shut off your computer and never turn it on again. That being said, always research the software you will be downloading and using, and always make sure it is from a trusted source. For instance, only download ChemDoodle from us, not from the strange site that very suspiciously has all of your favorite commercial applications for free.
The future of Java applets is clear, they should no longer be used. Doing a quick Google search for turning off Java applets in your browsers will provide instructions. If you are looking for a safe alternative to Java applets, investigate HTML5 solutions, such as the ChemDoodle Web Components library in chemistry. HTML5 technologies are based on Javascript (which has nothing to do with Java), and is a very safe programming language regulated by the browser developers.