1

There's a kind of a convoluted sentence in this text and it interested me. I became curious why the Present Perfect is used here.

Deriving a parsimonious evolutionary scenario is based on the premise that over time, genetic change is relentless, such that distant relatives are expected to have fewer features in common than close relatives (Koonin et al., 2001). Therefore, the presence of some distinguishing genetic signal in a distant relative but absent from more closely related organisms contradicts this expectation. The most common causes of these anomalies are loss of the genetic signal in close relatives or gene acquisition in a distant relative.

In practice, genomes provide a wealth of data that can be used as a source of distinctive features that have revealed unexpected relationships indicative of HGT. Some of these features include biochemical/biological properties (Pierce et al., 2003; Wenzl et al., 2005), recombination signals in closely related organisms (EscobarPáramo et al., 2004; Hakenbeck et al., 2001), presence of mobile genetic elements (MGEs) or viral sequences (Burrus and Waldor, 2004; Paulsen et al., 2003; Welch et al., 2002), gene content pattern (Hall et al., 2005; Hao and Golding, 2004; Homma et al., 2007; Hong et al., 2004; Korbel et al., 2002), presence/absence of genomic features (Gupta and Griffiths, 2002; Kroll et al., 1998; Snyder et al., 2007), database searches for nearest relatives (Aravind et al., 1998; Parkinson and Blaxter, 2003; Ragan and Charlebois, 2002) and unequal rates of genetic divergence (Bromham and Penny, 2003; Novichkov et al., 2004).

(From "Risks from GMOs due to Horizontal Gene Transfer", by Paul Keese)

Does the sentence with the bolded part mean

Genomes provide a wealth of data. This data has been sifted through by scientists looking for some new genomic features allowing to detect horisontal gene transfer (HGT) events. You can also sift this data through, and maybe you'll find a previously undescribed distinctive feature associated with HGT. Such a feature will reveal some new unexpected relationship, which you as a phylogenetics expert will know cannot be there if not for a past HGT event.

I mean, does the author use the Present Perfect in order to stress that this array of known distinctive features is not yet complete, and that genomes serve as a source for mining for new "distinctive features"?

Otherwhise, I would see no reason for not simplifying the sentence to

In practice, genomes provide a wealth of data that can be used as a source of distinctive features that speak of unexpected relationships indicative of HGT.

If the meaning would remain largely the same, then why make a convoluted sentence convolutier by introducing Present Perfect?


Or maybe the meaning is not "you can look for new distinctive features" but "you can look for features that have already been described"..

7
  • 1
    I think this have revealed is experiential. Sep 17 '15 at 18:11
  • @DamkerngT. - so the meaning is "you can analyze genomes to find features that have been described in the scientific literature so far"? And not "you can discover a novel distinctive feature of the kind that have been discovered so far"? It's a strange sentence.. Sep 17 '15 at 18:17
  • 1
    @CopperKettle The experiential sense of the present perfect is probably best demonstrated with It has happened before. Though it's unclear when such features revealed unexpected relationships indicative of HGT, and it's unclear how many times it have happened and weather or not it will happen again, I'd assume that have revealed is used to express the knowledge of the researcher that they knew that such revealing had happened before the time they wrote this paper. Sep 17 '15 at 18:29
  • 1
    "In practice, genomes provide a wealth of data that can be used as a source of distinctive features that have revealed unexpected relationships indicative of HGT." Genomes provide a wealth of data [relating to] distinctive features [some of which] have revealed unexpected relationships that suggest HGT is involved. Sep 17 '15 at 19:05
  • 1
    I don't expect nuance when I see a phrase like "data that can be used as a source of distinctive features that..." Sep 17 '15 at 19:14
3

SHORT ANSWER:
As a result of the distinctive features evident in genome data we now perceive many unexpected relationships which suggest that HGT in fact occurred in the past.

The author is not just mentioning historical events; he is citing historical events as the source of present (and, presumably, presently interesting) knowledge.

LONGER ANSWER:
The minimal meaning of the perfect is that some state (the 'perfect state') obtains at 'reference time', (in this case, the present) and that that state in some sense arises out of the prior (in this case, past) occurrence of the eventuality named by the lexical verb (in this case reveal).

It is left to the reader/hearer to infer what exactly the perfect state is; but it's ordinarily fairly easy to determine.

In this case the verb reveal signifies "cause [DIRECT OBJECT] to pass from the state of being invisible to the state of being visible". It is ordinarily assumed (absent some indication to the contrary) that any named state endures throughout the reference situation, so the reader/hearer infers in this case that the final state of being visible endures into the present and that that state is, fact, the 'present state' designated by the perfect construction.

This use of the perfect construction is called the resultative or stative perfect (perfect of result); it

indicates a single prior event whose result state is still current at Reference Time. —What is the perfect, and how should I use it?,3.2.1

The meaning, then, of the present perfect here is that many unexpected relationships [the direct object of reveal] are now visible.

There's a good deal of semantic ellipsis going on here, of course. For instance, to say that the data are a "source" of distinctive features is a shorthand way of saying that the distinctive features may be found and recognized in the data; to say that the features "reveal" relationships is a shorthand way of saying that analysis of the distinctive features shows the relationships to be present; and "reveal" is a shorthand way of saying "describe and publish for review by the scientific community.

Consequently, we may revise the paraphrase with which we started as:

Analysis of the distinctive features found in genome data has resulted in the publication of many unexpected relationships which suggest that HGT in fact occurred in the past.

And a list of representative relationships, with citations of the papers in which they are described, is what follows.

5
  • Thank you! Still the sentence as a whole seems illogical. "You can search genome data for distinctive features that have revealed unexpected relationships indicative of HGT". When I try to translate it into Russian, I stumble at "have revealed", because the sentence comes out illogical. Sep 18 '15 at 2:31
  • 1
    @CopperKettle Where are you getting "You can search"? You know that the data can be a source because it has been a source; there is no necessary futurive implication here. Sep 18 '15 at 2:41
  • "Where are you getting "You can search"?" - " a wealth of data that can be used as a source of distinctive features". The data can be used as a source of features that reveal unexpected relationships would've been more okay... Sep 18 '15 at 2:44
  • P.S. I also don't understand how database searches for nearest relatives can be a feature (in the big last sentence). On the face of it, looks like a downright error. Sep 18 '15 at 18:59
  • 1
    @CopperKettle Oh, sure, there's a lot of slovenly writing in there. But that has nothing to do with your question. Sep 18 '15 at 21:46

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.