这个是主语从句。it是形式主语，后面 what controls the flow of carbon dioxide in and out the atmosphere today.是真正的主语。由于主句里缺主语，又根据意思，所以要用what, that无意义。
意思是：如今，众所周知是什么控制着二氧化碳进出大气层。
英语,名词性从句 It is pretty well understood______controls the flow
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