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Here it says that the Future Perfect Continuous can be also used to predict what was happening in the past.

“What do you think the men were doing in the store room?” “Don’t worry. They will have been unpacking boxes.”

What do you think those men were doing in Charles’s garden yesterday? I expect they’ll have been doing some gardening.

  1. How come a future tense describes the past?
  2. Are there any good alternatives? I mean different tense for the particular exemplary sentences.
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The Future Perfect Continuous can be also used to predict what was happening in the past.

I don't think that predict is the best way to understand the construction being used here. To predict generally means to say what you think will happen in the future. But in the packing boxes and gardening examples there is no prediction about the future involved. Rather there is a supposition or assumption about the past.

Collins Cobuild English Grammar (p223) explains this particular use of will as follows:

You use 'will' when you are assuming that something is the case and you do not think there is any reason to doubt it.

  • Most listeners will have heard of hormones.

As an alternative to the use of will in your sentences, you could use the past continuous with probably (or as in the second case just leave the I expect to convey the probability):

  • What do you think the men were doing in the store room? - Don’t worry. They were probably unpacking boxes.

  • What do you think those men were doing in Charles's garden yesterday? I expect they were doing some gardening.

  • I agree that the future continuous implies probability and I think it works because both prediction and forming an opinion regarding probability of an event in the past both require extrapolation from incomplete data. Not only that but there is an implied prediction in expressing a probability, for example "I predict that, when you ask Charles what the men were doing, he will say that they were gardening." – BoldBen Mar 5 at 8:50
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    @BoldBen. You are right that you can construe the construction as a prediction about the future. But then the prediction will be about what Charles will say or what you will find out (should you ask). I think that using predict together with what was happening in the past is not the best way to help learners understand this construction. Better is: to express a likelihood or to make an assumption. – Shoe Mar 5 at 9:01

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