Proposed Terms - Revision history

Rarp at 22:29, 30 November 2008

2008-11-30T22:29:19Z

Rarp at 22:24, 30 November 2008

2008-11-30T22:24:51Z

Rarp at 22:22, 30 November 2008

2008-11-30T22:22:07Z

Rarp at 17:14, 30 November 2008

2008-11-30T17:14:21Z

Rarp at 02:29, 30 November 2008

2008-11-30T02:29:36Z

Rarp at 02:25, 30 November 2008

2008-11-30T02:25:27Z

Rarp at 02:03, 30 November 2008

2008-11-30T02:03:48Z

Rarp at 14:24, 25 November 2008

2008-11-25T14:24:18Z

Rarp at 00:17, 9 November 2008

2008-11-09T00:17:07Z

Rarp at 00:13, 9 November 2008

2008-11-09T00:13:24Z

@@ Line 668: / Line 668: @@
 OK?
 Bjoern Peters:  I like it.
 Werner Ceusters:  Seems OK. Still requires a note in the paper that 'clinically' is not related here to 'clinician'.
@@ Line 705: / Line 715: @@
 chemically abnormal, and
 musically abnormal.
 Bjoern Peters: 'clinically abnormal' should encompass '-+-' and '-++' in Werner's scheme, right? I thought about labels for a while, and am not happy with the following, but thought it was worth sharing, if only to inspire to do better:
 'health risk associated abnormality'
 Richard Scheuermann: While I agree with the components of the elucidation, I find the wording rather awkward.  Since this is an elucidation rather than a definition, couldn't we make it a little more intuitive for the average clinician scientist.  How about something like this:

@@ Line 702: / Line 702: @@
 Barry Smith: There might be:
-mechanically abnormal
+mechanically abnormal,
-chemically abnormal
+chemically abnormal, and
-musically abnormal
+musically abnormal.
 Bjoern Peters: 'clinically abnormal' should encompass '-+-' and '-++' in Werner's scheme, right? I thought about labels for a while, and am not happy with the following, but thought it was worth sharing, if only to inspire to do better:
@@ Line 720: / Line 720: @@
 How about:
-medically abnormal
+medically abnormal,
-abnormal condition
+abnormal condition, and
 pathologic?

← Older revision		Revision as of 22:22, 30 November 2008
Line 709:		Line 709:

	'health risk associated abnormality'		'health risk associated abnormality'
		+
		+	Richard Scheuermann: While I agree with the components of the elucidation, I find the wording rather awkward. Since this is an elucidation rather than a definition, couldn't we make it a little more intuitive for the average clinician scientist. How about something like this:
		+
		+	We use 'clinically abnormal' to characterize those bodily features of or in an organism that i) are causally linked to an elevated risk of pain or other feelings of illness, death or dysfunction), ii) are not part of the life plan for an organism of the relevant type (e.g. pregnancy or menopause), and iii) are such that the elevated risk exceeds a certain threshold level.
		+
		+	Also, Barry noted above:
		+
		+	"I would like to move to a position where 'clinical' means 'pertaining to what goes on in the clinic' (so: 'clinical exam', 'clinical manifestation' ...). Can we find an alternative for 'clinical' in the term 'clinically abnormal'?"
		+
		+	How about:
		+
		+	medically abnormal
		+	abnormal condition
		+	pathologic?

@@ Line 641: / Line 641: @@
 -----
-Returning to Bjoern's issues with our tripartite definition of clinically abnormal (see below). I agree with Bjoern that it would be much nice if we could just use Part (1). Unfortunately, 'elevated level of risk' is a continuous function, and there are some very low levels of elevation (a tiny pin prick) which will not be judged to be clinically significant. Part (2) is introduced to do justice to the need to create a threshold between the insignificant and the significant levels of elevatedness.
+Barry Smith: Returning to Bjoern's issues with our tripartite definition of clinically abnormal (see below). I agree with Bjoern that it would be much nice if we could just use Part (1). Unfortunately, 'elevated level of risk' is a continuous function, and there are some very low levels of elevation (a tiny pin prick) which will not be judged to be clinically significant. Part (2) is introduced to do justice to the need to create a threshold between the insignificant and the significant levels of elevatedness.
 I propose a modified version below, simplified in light of Bjoern's recommendation, that is designed to remove the appearance of subjectivity from our original statement, and to eliminate the interpretation according to which clinical abnormality might come into existence because clinicians adopt certain beliefs.
@@ Line 647: / Line 647: @@
 At 03:33 PM 11/5/2008, Bjoern Peters wrote:
-Peters: I agree with all of Werner's points, but I didn't think that is written in the paper. This is the section I am referring to.  Clinically abnormal is classified as a primitive term, with the following informal elucidation which I split it into three parts:
+Bjoern Peters: I agree with all of Werner's points, but I didn't think that is written in the paper. This is the section I am referring to.  Clinically abnormal is classified as a primitive term, with the following informal elucidation which I split it into three parts:
 (1) "We use 'clinically abnormal' to characterize those bodily features of or in an organism that are causally linked to an elevated risk of pain or other feelings of illness, to dysfunction, or to enhanced morbidity, and which (unlike pregnancy or
@@ Line 669: / Line 669: @@
 OK?
-Peters:  I like it.
+Bjoern Peters:  I like it.
 Werner Ceusters:  Seems OK. Still requires a note in the paper that 'clinically' is not related here to 'clinician'.
@@ Line 706: / Line 706: @@
 musically abnormal
-Peters: 'clinically abnormal' should encompass '-+-' and '-++' in Werner's scheme, right? I thought about labels for a while, and am not happy with the following, but thought it was worth sharing, if only to inspire to do better:
+Bjoern Peters: 'clinically abnormal' should encompass '-+-' and '-++' in Werner's scheme, right? I thought about labels for a while, and am not happy with the following, but thought it was worth sharing, if only to inspire to do better:
 'health risk associated abnormality'

@@ Line 627: / Line 627: @@
 Is this satisfactory?
-Lindsay: maybe ... i guess the question is whether in all cases, the inability for a normal process to unfold results in a pathological process, and even if yes, is the disease only realized through the pathological process?  the example i was thinking of (and i will try to think of others) is SCID (severe combined immunodeficiency).  there are different underlying disorders, but the one i am thinking of is mutations in the RAG1 or RAG2 genes.  in this case, the process of V(D)J recombination cannot be realized so B cells and T cells do not develop and the patients cannot mount adaptive immune responses.  in this case, because the patients' immune responses are not normal, we can say that the disease is realized in a pathological immune response, so you are right, the definition still works.  but what i was thinking at the time, and what i still have as a question, is maybe in this case the disease is realized through the fact that V(D)J recombination does not happen.  (and the pathological immune response is the realization of a different disease, the infectious disease.)
+Lindsay: Maybe.  I guess the question is whether in all cases, the inability for a normal process to unfold results in a pathological process, and even if yes, is the disease only realized through the pathological process?  The example I was thinking of (and I will try to think of others) is SCID (severe combined immunodeficiency).  There are different underlying disorders, but the one I am thinking of is mutations in the RAG1 or RAG2 genes.  In this case, the process of V(D)J recombination cannot be realized, so B cells and T cells do not develop and the patients cannot mount adaptive immune responses.  In this case, because the patients' immune responses are not normal, we can say that the disease is realized in a pathological immune response, so you are right, the definition still works.  But what I was thinking at the time, and what I still have as a question, is maybe in this case the disease is realized through the fact that V(D)J recombination does not happen.  (And the pathological immune response is the realization of a different disease, the infectious disease.)
-there may be other diseases in which there is no ensuing pathological process (like the pathological immune response) and so are better examples of my concern.  or maybe there is no need for my concern because there is always some pathological response.  i am not sure.
+There may be other diseases in which there is no ensuing pathological process (like the pathological immune response) and so are better examples of my concern.  Or maybe there is no need for my concern because there is always some pathological response.  I am not sure.
 Barry Smith: My hypothesis is that, if there is no pathological process (including for example slowed growth), then we would not talk of disease.
@@ Line 671: / Line 671: @@
 Peters:  I like it.
-Werner Ceusters:  Seems ok. Still requires a note in the paper that 'clinically' is not related here to 'clinician'.
+Werner Ceusters:  Seems OK. Still requires a note in the paper that 'clinically' is not related here to 'clinician'.
 Barry Smith: I would like to move to a position where 'clinical' means 'pertaining to what goes on in the clinic' (so: 'clinical exam', 'clinical manifestation' ...). Can we find an alternative for 'clinical' in the term 'clinically abnormal'?
-Werner Ceusters: Do you need an adjective ?  What others sorts of abnormality are there? I can think of normal variants (non-canonical, non-pathological ones).
+Werner Ceusters: Do you need an adjective?  What other sorts of abnormality are there?  I can think of normal variants (non-canonical, non-pathological ones).
 Perhaps we need these dimensions:

@@ Line 620: / Line 620: @@
 Barry:  Yes.
 -----
@@ Line 654: / Line 668: @@
 OK?

← Older revision		Revision as of 02:03, 30 November 2008
Line 620:		Line 620:

	Barry: Yes.		Barry: Yes.
		+
		+	-----
		+	From: "Smith, Barry" [mailto:phismith@buffalo.edu]
		+	Sent: 11/27/2008
		+	Subject: RE: Follow-up Information Regarding the Dallas Workshop on Clinical Phenotypes
		+	-----
		+
		+	Returning to Bjoern's issues with our tripartite definition of clinically abnormal (see below). I agree with Bjoern that it would be much nice if we could just use Part (1). Unfortunately, 'elevated level of risk' is a continuous function, and there are some very low levels of elevation (a tiny pin prick) which will not be judged to be clinically significant. Part (2) is introduced to do justice to the need to create a threshold between the insignificant and the significant levels of elevatedness.
		+
		+	I propose a modified version below, simplified in light of Bjoern's recommendation, that is designed to remove the appearance of subjectivity from our original statement, and to eliminate the interpretation according to which clinical abnormality might come into existence because clinicians adopt certain beliefs.
		+
		+	At 03:33 PM 11/5/2008, Bjoern Peters wrote:
		+
		+	Peters: I agree with all of Werner's points, but I didn't think that is written in the paper. This is the section I am referring to. Clinically abnormal is classified as a primitive term, with the following informal elucidation which I split it into three parts:
		+
		+	(1) "We use 'clinically abnormal' to characterize those bodily features of or in an organism that are causally linked to an elevated risk of pain or other feelings of illness, to dysfunction, or to enhanced morbidity, and which (unlike pregnancy or
		+	menopause) are not such as to belong to the life plan for an organism of the relevant type."
		+
		+	(2) A clinician will judge a bodily feature to be clinically abnormal only where the elevated risk exceeds a certain threshold level of clinical significance. The determination of this threshold will reflect the training and experience of the clinician in question and thus may vary from clinical context to clinical context.
		+
		+	(3) It is worth noting that this treatment of 'normality' is distinct from those statistical treatments which do not take account of overlap of parameter values used to distinguish between normal and abnormal or of distribution extremes."
		+
		+	(1) is great, and all I would want to say, given how the term is used throughout the paper.
		+	(2) is minimally confusing. Being generous, I can accept that this is no longer talking about 'clinically abnormal', but about the judgment of a physician thereof which is a completely different entity. That does make the 'clinically' part of the label suspect though, and I don't think it helps to understand the term better.
		+	(3) So what is this? Does it refer to the treatment of 'normality' for (1) or (2)?
		+
		+	Barry Smith: We use 'clinically abnormal' to characterize those bodily features of or in an organism that
		+	i) are causally linked to an elevated risk of (pain or other feelings of illness or of death or of dysfunction),
		+	ii) are unlike pregnancy or menopause in being not such as to belong to the life plan for an organism of the relevant type,
		+	iii) are such that the elevated risk exceeds a certain threshold level.
		+
		+	This would replace (1) and (2).
		+
		+	OK?

← Older revision		Revision as of 14:24, 25 November 2008
Line 600:		Line 600:

	Thanks to all for the careful evaluation. I suspect that we will definitely need to do a little wordsmithing in order to make these points more clearly.		Thanks to all for the careful evaluation. I suspect that we will definitely need to do a little wordsmithing in order to make these points more clearly.
		+
		+	-----
		+	From: "Cowell, Lindsay" [mailto:cowel011@mc.duke.edu]
		+	Sent: 11/24/2008
		+	Subject: RE: Follow-up Information Regarding the Dallas Workshop on Clinical Phenotypes
		+	-----
		+
		+	Lindsay Cowell: In general, I think the draft is well written and the definitions good. I have just a couple of comments/questions:
		+
		+	1. Disease is defined (partly) as the disposition to undergo certain pathological processes. It seems we should also take into account diseases that result from the inability to undergo certain normal processes. So there is the absence of a process where there should be one.
		+
		+	Barry Smith: We will fix that.
		+
		+	Lindsay: 2. A predisposition has as its physical basis a disorder, which is a physical structure, according to the definitions. And this makes sense I think. But in the bit of clarifying text that follows the definition, you say that a predisposition is a disposition to acquire further dispositions and that diseases may be predispositions. These two statements seem to be a mixing of independent and dependent continuants.
		+
		+	Barry: You are right, we will fix that.
		+
		+	Lindsay: 3. It might be better to say that the predisposition confers on the organism the disposition to acquire further dispositions (or disorders), and that diseases may result in such predisposing disorders.
		+
		+	Barry: Yes.

@@ Line 560: / Line 560: @@
 WC: Such thresholds, as you would have it, are again level 2 entities.  Thresholds for whether
 something is clinically abnormal or not do exist also at level 1.  An informed clinician's assessment of level 1 thresholds would be probably better than an uninformed one, but it remains an assessment.
 -----
@@ Line 598: / Line 582: @@
 Did you consider 'physiologically abnormal' or 'pathological' instead of 'clinically abnormal'?

@@ Line 585: / Line 585: @@
 I agree with all of Werner's points, but I didn't think that is written in the paper. This is the section I am referring to. Clinically abnormal is classified as a primitive term, with the following informal elucidation, which I split it into three parts:
-) "We use 'clinically abnormal' to characterize those bodily features of or in an organism that are causally linked to an elevated risk of pain or other feelings of illness, to dysfunction, or to enhanced morbidity, and which (unlike pregnancy or menopause) are not such as to belong to the life plan for an organism of the relevant type."
+(1) "We use 'clinically abnormal' to characterize those bodily features of or in an organism that are causally linked to an elevated risk of pain or other feelings of illness, to dysfunction, or to enhanced morbidity, and which (unlike pregnancy or menopause) are not such as to belong to the life plan for an organism of the relevant type."
-) "A clinician will judge a bodily feature to be clinically abnormal only where the elevated risk exceeds a certain threshold level of clinical significance. The determination of this threshold will reflect the training and experience of the clinician in question and thus may vary from clinical context to clinical context."
+(2) "A clinician will judge a bodily feature to be clinically abnormal only where the elevated risk exceeds a certain threshold level of clinical significance. The determination of this threshold will reflect the training and experience of the clinician in question and thus may vary from clinical context to clinical context."
-) "It is worth noting that this treatment of 'normality' is distinct from those statistical treatments which do not take account of overlap of parameter values used to distinguish between normal and abnormal or of distribution extremes."
+(3) "It is worth noting that this treatment of 'normality' is distinct from those statistical treatments which do not take account of overlap of parameter values used to distinguish between normal and abnormal or of distribution extremes."
-) is great, and all I would want to say, given how the term is used throughout the paper
+Regarding (1), it is great, and all I would want to say, given how the term is used throughout the paper.
-) is minimally confusing. Being generous, I can accept that this is no longer talking about 'clinically abnormal', but about the judgment of a physician thereof which is a completely different entity. That does make the 'clinically' part of the label suspect though, and I don't think it helps to understand the term better.
+Regarding (2), it is minimally confusing. Being generous, I can accept that this is no longer talking about 'clinically abnormal', but about the judgment of a physician thereof which is a completely different entity. That does make the 'clinically' part of the label suspect though, and I don't think it helps to understand the term better.
-) So what is this? Does it refer to the treatment of 'normality' for 1) or 2)?
+Regarding (3), what is this? Does it refer to the treatment of 'normality' for (1) or (2)?
 Did you consider 'physiologically abnormal' or 'pathological' instead of 'clinically abnormal'?