You’ve asked about the verbs used in your quoted paragraph’s last sentence.
Among patients in his study, “some of them had gotten flu in the past, and
we’re looking to see if the autoantibodies could have had an effect on flu.”
There are no conditionals here at all, just a modal perfect past in keeping
with the perfect past form of the had gotten verb used earlier in that
The rest of this post explains why this has been done and how you can
predict and generate similar clauses for yourself. The Addendum at the bottom illustrates why your choices in terminology are confusing and limiting you because they do not fairly model how English grammar really works.
What you have here is a case of the verb to see X, where X is the finite
clause “if the autoantibodies could have had an effect on flu”.
Whenever the object of the transitive verb see is a wh- clause like
this (sometimes called an “interrogative” clause), the meaning of the
matrix verb per the Oxford English Dictionary is equivalent to:
To ascertain or establish by observation, inquiry, or reflection; to investigate.
Or more fully, letting the word something stand in for your X clause:
To ascertain [something] or establish [something] by observation, inquiry, or reflection; to investigate [something].
This wh- clause here is necessarily a complement clause because it serves
as the transitive verb’s complement: its object. So sure, I reckon you can
call it an “object clause” if you’d like. This sentence therefore means
the same thing as the original:
Among patients in his study, “some of them had gotten flu in the past, and
we intend to investigate whether the autoantibodies could have had an effect on flu.”
In fact, this version, which doesn’t use a formal modal at all, also means
the very same thing as the original:
Among patients in his study, “some of them had gotten flu in the past, and
we are planning on investigating whether the autoantibodies had been able to affect flu.”
But exactly why those are equivalent will require a bit of explanation, given below.
Modal Verbs: Dual Modalities
This complement clause’s modal verb could (which is just the past tense of can)
is here being used in the epistemic mode of prediction, not in the deontic
mode of obligation.
Instead of being a plain infinitive like to affect (which is all that the phrasal verb to
have an effect on means), this instance is further marked with the perfective
aspect by using a “perfect infinitive” as you call it by using to have
with the perfect/past participle of that verb.
Here just like anywhere else they’re used, a modal verb adds nuance by
altering the “modality” of the verb following it. Instead of a simple
statement of plain fact, it becomes one of either prediction or obligation. It is
either a predictive statement about the possible or probable world (the
so-called “epistemic mode”), or else it is a statement of how the world
ought to be or become (the so-called “deontic mode”) in keeping with
the speaker’s or society’s desires, demands, or norms.
It’s not just the modal verb could that does this shading of reality away
from a simple indicative sense. All modal verbs do this, because that is
their purpose. However, there is a problem with modal verbs. Compared with
normal verbs, the nine English modals (will/would, shall/should, can/could, may/might, and must) are all defective in multiple ways.
For one, they
never inflect for person or number.
For another, they lack corresponding
non-finite forms such as infinitives and participles.
And to some extent,
they even lack inflections for the past tense because although you can
backshift some of them for tense like can to could, this is more an
obligatory shift than a deliberate one, and the modal must has no
past-tense version. That means that it’s hard to convey tense in a modal,
and that whenever we need some non-finite version of a modal like its
infinitive or a participle, it’s the verb following that modal that takes on
the non-finite form.
For example, here we’ll use may/might in the epistemic mode of simple prediction:
- He thinks that she may be hungry. (plain present)
- He thought that she might be hungry. (plain past)
- He has thought that she may have been hungry. (perfect present)
- He had thought that she might have been be hungry. (perfect past)
Or, if we want, sometimes we can do something else altogether.
We can find
some sort of periphrastic version using normal verbs to which we can then
apply normal verbal inflections. Because another rule about modals is that
you can only have one per verb phrase, we also have to use a periphrastic
rephrasing whenever we want to apply more than one modal at a time (at least
in standard English).
That’s why the can in can affect gets rewritten
into be able to when we need to talk about something in the future,
leaving us with constructions like will be able to affect.
Unconditional Modal Perfects
I have explained all this, and done so in this fashion, because it allows
me to answer your question about how to understand the verbal patterns
that allow us to generate could and perfect infinitives in places
other than in conditional clauses alone.
So now let’s get back to your complement clause and see just exactly
what’s happening in it. Its subject is antibodies and the verb
in general is to have an effect on, which is simply a phrasal-verb version of
- to have an effect on X = to affect X (plain infinitive)
- to have had an effect on X = to have affected X (perfect infinitive)
This leads to four ways of writing that verb. It can be in the present (or at least, the non-past)
or the past, and it can be either plain or perfect.
- autoantibodies have an effect on = autoantibodies affect (plain present)
- autoantibodies had an effect on = autoantibodies affected (plain past)
- autoantibodies have had an effect on = autoantibodies have affected (perfect present)
- autoantibodies had had an effect on = autoantibodies had affected (perfect past)
But now we need to use the modal could here. This is what leads to the perfect
infinitive, because modals always take infinitives:
- autoantibodies can have an effect on = autoantibodies can affect (plain present)
- autoantibodies could have an effect on = autoantibodies could affect (plain past)
- autoantibodies can have had an effect on = autoantibodies can have affected (perfect present)
- autoantibodies could have had an effect on = autoantibodies could have affected (perfect past)
Now let’s do one more rewrite for illustration. Instead of using modal can/could X,
we’ll use the periphrastic modal to be able to X.
- autoantibodies are able to have an effect = autoantibodies are able to affect (plain present)
- autoantibodies were able to have an effect = autoantibodies were able to affect (plain past)
- autoantibodies have been able to have an effect = autoantibodies have been able to affect (perfect present)
- autoantibodies had been able to have an effect = autoantibodies had been able to affect (perfect past)
So in saying that “the autoantibodies could have had an effect on flu”, this
means the very same thing as “the autoantibodies had been able to affect
So there is nothing at all “conditional” involved here, despite your clause
using a modal perfect. Why would there be? It is simply a backshifted
epistemic modal used to make a prediction about a possibility, and the
reason it’s used with a perfect infinitive is so that it reflects the same
narrative time as had gotten flu from the earlier part of the sentence,
and had gotten is in the perfect past. Therefore this one needs to be in
the perfect past as well.
If we simplify had gotten flu from the perfect past into the plain past
version got flu (or the equivalent and more common had the flu), we can
also simplify the remaining verb phrase to match:
Among patients in his study, “some of them had the flu in the past, so
we’re looking to investigate whether those autoantibodies had been able to affect flu.”
Or even more simply:
Among patients in his study, “some of them got the flu in the past, so
we’re investigating whether those earlier autoantibodies affected later bouts with the flu.”
There are no conditionals here at all, just modal past perfects to fit
with the past perfect from earlier in that same sentence.
Addendum: Unconstructive Models
Your mention of subjunctive mood and type-three conditional strongly
suggest to me that you’ve been taught that these are terms that can be
meaningfully applied to English. This may be where you’ve been led astray.
Although under some linguistic models, such terms can sometimes be bent
into English service, it is at best an unnatural and ill-fitting servitude bitterly indentured. Those terms
do not really apply to English. Instead, you have to learn how we actually
use modals here.
There is nothing about modal verbs in English that restricts their use to
only subordinate or complement clauses instead of main clauses. All that
happens when you use a modal is that it makes a verb something other than
strictly real. But please do not call it “subjunctive”. Call it modal.
Just as soon as you pull in a modal, though, your verb stops being real and becomes
“modal” instead. So you should contrast real verbs with modal verbs in
English, not indicative with subjunctive. Once it’s modal it’s no longer
in the real mode, but whether it’s the epistemic mode or the deontic mode
strictly varies by the speaker’s intent. Both modes are always possible.
And we have a whole lot of different modal verbs, not just the nine
standard ones and the three or four semi-modals that come quickly to mind, but also gobs and gobs of
periphrastic modals as well like used to and has to and is to and is supposed
to and is able to, and many more besides.
Let’s use the verb sing, and first talk about the reals. As a finite verb
you might use in a main clause, you always have four variants for real
(“non-modally marked”) constructions:
- She sings. (plain present: real)
- She sang. (plain past: real)
- She has sung. (perfect present: real)
- She had sung. (perfect past: real)
Just like any real verb, any modal verb also comes in those same four basic
flavors: plain-vs-perfect (sometimes called simple-vs-perfect) and present/nonpast-vs-past.
- She will sing. (plain present: modal)
- She would sing. (plain past: modal)
- She will have sung. (perfect present: modal)
- She would have sung. (perfect past: modal)
You can do that same with any of the modals.
- She can sing. (plain present: modal)
- She could sing. (plain past: modal)
- She can have sung. (perfect present: modal)
- She could have sung. (perfect past: modal)
In the same way, they can all also be used not just as the main clause but
in complement clauses or subordinate clauses. First the real versions
as complement clauses:
- I think she sings opera. (plain present: real)
- I thought she sang opera. (plain past: real)
- I have thought she has sung opera. (perfect present: real)
- I had thought she had sung opera. (perfect past: real)
Then the corresponding modal versions as complement clauses:
- I do not think she can sing opera. (plain present: modal)
- I did not think she could sing opera. (plain past: modal)
- I have not thought she can have sung opera. (perfect present: modal)
- I had not thought she could have sung opera. (perfect past: modal)
There’s nothing special about complement clauses; you can
do all those same things as subordinate clauses as well.
First as reals:
- She always sings opera if she wants to. (plain present: real)
- She always sang opera if she wanted to. (plain past: real)
- She has always sung opera if she has wanted to. (perfect present: real)
- She had always sung opera if she had wanted to. (perfect past: real)
And then as modals:
- She will sing opera if she wants. (plain present: modal)
- She would sing opera if she wanted. (plain past: modal)
- She will have sung opera if she has wanted. (perfect present: modal)
- She would have sung opera if she had wanted. (perfect past: modal)
As you see, there is nothing about the use of real-vs-modal verbs in
complement clauses or in subordinate clauses that is in any way special
compared with how the same real-vs-modal verbs get used in main clauses.
And all those same things remain true no matter whether these are simple
uses or perfective uses in every case.
The “zero” modal + infinitive
Verbs marked with a modal are always unreals, not reals. This is true even for the “zero modal” case:
- They demand that she leave. (real present followed by bare infinitive as an untensed unreal prefaced by the zero modal)
- They demanded that she leave. (real past followed by bare infinitive as an untensed unreal prefaced by the zero modal)
As you see, the verb leave is used there in the bare infinitive, just as though it were preceded by an actual modal verb before it. It can be useful under this model of synchronic
analysis to consider it an instance of a zero-modal plus an infinitive. This isn’t much of a marker beyond signaling that it is not real, that it is an unreal case. As modals go, the zero modal is a deontic one because it is making a statement about how the world ought to be.
Under diachronic analysis this derives from what in Old English had been the present subjunctive, but that analysis doesn’t make sense synchronically. It really is not marked for tense at all, since both they demand and they demanded take the same bare infinitive unmarked for tense when used with the hypothesized zero modal.
Sometimes this is called the “mandative subjunctive” these days, but really it is a zero-modal plus a bare infinitive. It can no longer be used in the main clause, only in subordinate clauses or complement clauses.
The ancient, formulaic blessings and cursings did once upon a time take this form in the main clause to create a sort of “third-person imperative” (God bless you, God save the queen, Devil take the hindmost) but these are no longer productive in present-day English. Nowadays we instead use an explicit auxiliary verb like may or let for these types if we ever need to generate new ones: May the Force be with you!
The only non-modal unreal
Although all modals are unreals, not quite all unreals are modals. There is one non-modal unreal. The verb be retains a specially marked non-modal unreal inflection: were, which is invariant by person and number. Although under an historical diachronic analysis, it derives from what had been a past subjunctive form in Old English, under synchronic analysis it is just a special unreal form. It’s used in just a very few places, all strongly hypothetical in nature. Here is an assortment of those:
- Imagine it were so.
- He acted as if she were here.
- If only she were here.
- I wish this were easier.
- She would have left us a note if she were ready to leave.
- Unless she were ready, she would leave us no note.
Again, these are all unreal hypotheticals that are unreal by virtue of the unique were inflection instead of via a modal verb plus an infinitive as you must do for all other verbs except for be alone.
That’s why people sometimes rephrase certain kinds of “if I said X...” clauses into the periphrastic inflected-be + to-infinitive version: “if I were to say X...” The reason we sometimes do this is because the second feels more hypothetical than the first does due to its overt inflectional “unreality” signal.
Summary of Addendum
Don’t get wrapped up in terms like subordinate mood or type-three conditionals,
because these are not useful models for describing English grammar.
Instead, think about real verb constructions versus modal verb constructions,
and about simple verb constructions versus perfective verb constructions.
And definitely do not think of any of these as restricted to niche uses.
They are all found in main verb clauses, in subordinate verb clauses, and
in complement clauses. The real-vs-modal choices and simple-vs-perfect
choices you make in all three of those clause types are freely elected
depending on the speaker’s intent.
Now factor in how there isn’t just one modal the way languages with a
subjunctive inflection have just one of those to go with the real
indicative, but rather there are nine modals and perhaps a half-dozen
semi-modals and still more periphrastic modals on top of those two sets.
Double all that by understanding every one of those many modals is
dual-minded in that they can all equally express both epistemic and deontic
What this provides you with is hundreds and hundreds, perhaps even
thousands, of combinations available to the native speaker to produce
incredibly many subtle nuances, nuances which no simplistically dualistic
indicative-vs-subjunctive feature contrast alone can ever hope to approach let alone match.