Is it permissible to pay the registration fees for a scientific conference that includes a program of lunch meals with alcohol, knowing that the sole purpose of attending is for scientific benefit?

It is not permissible to pay fees that include the price of alcohol, because one of the conditions for the validity of a sales contract is that the sold item must be pure and permissible, and alcohol is neither. If these fees are paid, it means that you are authorizing the conference organizers to purchase alcohol for you, which is forbidden. Furthermore, this registration involves an endorsement and acceptance of a reprehensible act.

If possible, address the organizing body regarding the impermissibility of purchasing alcohol or sitting at tables where it is served. If they agree to allow you to pay the fees for a permissible drink, or if they deduct the price of alcohol for you, or if you can send only the registration fees and the price of the permissible items, then there is no harm. Otherwise, do not participate, even if it means you will not attend. A Muslim must adhere to their religion and not compromise on it.

If you are able to participate after the condition of alcohol is dropped, then be careful not to sit at a table where alcohol is served.