Background Flexible video bronchoscopes, in particular the Olympus BF Type 3C160, are commonly used in pediatric respiratory medicine. There is no data on the magnification and distortion effects of these bronchoscopes yet important clinical decisions are made from the images. The aim of this study was to systematically describe the magnification and distortion of flexible bronchoscope images taken at various distances from the object.
Background
Flexible video bronchoscopes, in particular the Olympus BF Type 3C160, are commonly used in pediatric respiratory medicine. There is no data on the magnification and distortion effects of these bronchoscopes yet important clinical decisions are made from the images. The aim of this study was to systematically describe the magnification and distortion of flexible bronchoscope images taken at various distances from the object.Methods Using images of known objects and processing these by digital video and computer programs both magnification and distortion scales were derived.
Methods
Using images of known objects and processing these by digital video and computer programs both magnification and distortion scales were derived.Results Magnification changes as a linear function between 100 mm (×1) and 10 mm (×9.55) and then as an exponential function between 10 mm and 3 mm (×40) from the object. Magnification depends on the axis of orientation of the object to the optic axis or geometrical axis of the bronchoscope. Magnification also varies across the field of view with the central magnification being 39% greater than at the periphery of the field of view at 15 mm from the object. However, in the paediatric situation the diameter of the orifices is usually less than 10 mm and thus this limits the exposure to these peripheral limits of magnification reduction. Intraclass correlations for measurements and repeatability studies between instruments are very high, r = 0.96. Distortion occurs as both barrel and geometric types but both types are heterogeneous across the field of view. Distortion of geometric type ranges up to 30% at 3 mm from the object but may be as low as 5% depending on the position of the object in relation to the optic axis.
Results
Magnification changes as a linear function between 100 mm (×1) and 10 mm (×9.55) and then as an exponential function between 10 mm and 3 mm (×40) from the object. Magnification depends on the axis of orientation of the object to the optic axis or geometrical axis of the bronchoscope. Magnification also varies across the field of view with the central magnification being 39% greater than at the periphery of the field of view at 15 mm from the object. However, in the paediatric situation the diameter of the orifices is usually less than 10 mm and thus this limits the exposure to these peripheral limits of magnification reduction. Intraclass correlations for measurements and repeatability studies between instruments are very high, r = 0.96. Distortion occurs as both barrel and geometric types but both types are heterogeneous across the field of view. Distortion of geometric type ranges up to 30% at 3 mm from the object but may be as low as 5% depending on the position of the object in relation to the optic axis.Conclusion We conclude that the optimal working distance range is between 40 and 10 mm from the object. However the clinician should be cognisant of both variations in magnification and distortion in clinical judgements.
Conclusion
We conclude that the optimal working distance range is between 40 and 10 mm from the object. However the clinician should be cognisant of both variations in magnification and distortion in clinical judgements.

Introduction The flexible bronchoscope has been used in pediatrics for more than 20 years [ 1 ] yet there are only a limited number of publications on the systematic examination of the physical properties of magnification and distortion found in endoscopes of any size, let alone bronchoscopes specific for the pediatric sized airways. [ 1 - 6 ]. Some understanding of specific bronchoscopic magnification and distortion is an important issue to the clinician as these instruments are being used more regularly to define the nature and severity of airway lesions such as tracheal stenosis and malacia disorders from which important medical and surgical decisions ultimately follow[ 7 - 14 ]. The pediatric bronchoscope comes in a variety of sizes but the resultant magnification from these instruments depends not only on the size but also on the image processing that occurs. Magnification of an object refers to the virtual or real visualized and measured increase in size of that object after rays of light from that object have passed through a lens system. Magnification varies across the field of view and with the distance of the lens from the object [ 15 ]. Distortion refers to the variations of the faithful representation in scale and perspective of the various elements of the object and its plane of context[ 15 ]. There are various forms of distortion including geometrical, curvilinear, anamorphic and perspective distortion recognised in photometrics [ 15 ]. Geometrical distortion refers to the changes in the peripheral details because of elongation of the elements of an object. Simply, it refers to the distortion that is created when there is increasing obliquity of the angle of viewing of the object. Curvilinear distortion is described where straight lines are rendered as curved either inward (pincushion) or outwards (barrel) curves. This form of distortion is a result of asymmetry of lens configuration and is a feature of bronchoscopes and indeed most endoscopes in general[ 2 , 5 , 16 ]. The ultimate image quality of any bronchoscope is dependent on the lens characteristics in general and the subsequent transmission of the image to the image processor and display module. The more recently developed bronchoscopes such as the flexible videobronchoscope (FVB's) have moved away from fibreoptics to transmit images. They use charge coupled devices (CCD's) which are mounted adjacent to the lens thus essentially converting the image to electrical energy at the lens. This early conversion of the image has the effect of producing "less noise" thus allowing greater image clarity. Despite the latter, all of these issues mentioned are important to the clinical use of FVB's and subsequent patient management and as the Olympus company was unable to provide the necessary details on magnification and distortion, we undertook to quantify these effects in order to enhance our decision making quality during FVB procedures. The aim of this paper is to define the magnification and distortion in a commonly used pediatric video bronchoscope: the Olympus BF Type 3C160.
Introduction
The flexible bronchoscope has been used in pediatrics for more than 20 years [ 1 ] yet there are only a limited number of publications on the systematic examination of the physical properties of magnification and distortion found in endoscopes of any size, let alone bronchoscopes specific for the pediatric sized airways. [ 1 - 6 ]. Some understanding of specific bronchoscopic magnification and distortion is an important issue to the clinician as these instruments are being used more regularly to define the nature and severity of airway lesions such as tracheal stenosis and malacia disorders from which important medical and surgical decisions ultimately follow[ 7 - 14 ]. The pediatric bronchoscope comes in a variety of sizes but the resultant magnification from these instruments depends not only on the size but also on the image processing that occurs.Magnification of an object refers to the virtual or real visualized and measured increase in size of that object after rays of light from that object have passed through a lens system. Magnification varies across the field of view and with the distance of the lens from the object [ 15 ]. Distortion refers to the variations of the faithful representation in scale and perspective of the various elements of the object and its plane of context[ 15 ]. There are various forms of distortion including geometrical, curvilinear, anamorphic and perspective distortion recognised in photometrics [ 15 ]. Geometrical distortion refers to the changes in the peripheral details because of elongation of the elements of an object. Simply, it refers to the distortion that is created when there is increasing obliquity of the angle of viewing of the object. Curvilinear distortion is described where straight lines are rendered as curved either inward (pincushion) or outwards (barrel) curves. This form of distortion is a result of asymmetry of lens configuration and is a feature of bronchoscopes and indeed most endoscopes in general[ 2 , 5 , 16 ]. The ultimate image quality of any bronchoscope is dependent on the lens characteristics in general and the subsequent transmission of the image to the image processor and display module. The more recently developed bronchoscopes such as the flexible videobronchoscope (FVB's) have moved away from fibreoptics to transmit images. They use charge coupled devices (CCD's) which are mounted adjacent to the lens thus essentially converting the image to electrical energy at the lens. This early conversion of the image has the effect of producing "less noise" thus allowing greater image clarity. Despite the latter, all of these issues mentioned are important to the clinical use of FVB's and subsequent patient management and as the Olympus company was unable to provide the necessary details on magnification and distortion, we undertook to quantify these effects in order to enhance our decision making quality during FVB procedures. The aim of this paper is to define the magnification and distortion in a commonly used pediatric video bronchoscope: the Olympus BF Type 3C160.Methods Equipment A flexible bronchoscope (Olympus BF Type 3C160, Olympus, Tokyo, Japan) and light source (Olympus Evis Exera CLV-160, Olympus, Tokyo, Japan) and processor (Olympus Evis Exera CV-160, Olympus, Tokyo, Japan) were connected to a TV monitor (Sony HR Trinitron, Sony Corporation, Shinagawa-ku, Tokyo, Japan) and a colour video printer (Sony Mavigraph, Sony Corporation, Shinagawa-ku, Tokyo, Japan) as supplied by the Olympus company. The image signals from the Evis Exera CV-160 were co-recorded by a digital camera (Sony Mini DV Digital Handycam, Sony Corporation, Shinagawa-ku, Tokyo, Japan). These digital video images were viewed and stored as uncompressed 640 × 480 pixel, millions of colours as TIFF files. These images were then analysed by an image processing program (Image J, Wayne Rasband, National Institute of Health, USA) and a computer (MAC Power Book G4. Apple Inc,, Cupertino, Ca., USA). Measurement of Magnification and Distortion A precisely measured object consisting of 4 concentric circles with emanating radii on 1 mm × 1 mm graph paper was created and drawn to precision using design software (Auto CAD, Autodesk, San Rafael, Ca, USA) (Fig  1 ). These circles were 2, 6, 10 and 20 mm diameter respectively. A precision made device that fixed the hand piece and supported the length of the bronchoscope so that the central or geometric axis of the bronchoscope (Fig.  2 ) would align with the centre point of a moveable screen was engineered by Queensland Radium Institute (QRI, Brisbane, Australia) engineering. The device's moveable stage allowed the object to be positioned over a range of distances from 100 mm to 3 mm without moving the scope itself. The measured distances were verified with electronic callipers to a degree of accuracy of 0.02 mm. The calibration process for calculation of magnification and distortion was performed at the distance of 100 mm, the point at which the object to image ratio was 1. All subsequent ratios were therefore larger than the calibration value and represented the magnification of the object. Figure 1 Photographic Object: A square of graph paper 3 cms × 3 cms with 1 mm × 1 mm units and concentric circles of varying diameter (2 mm, 6 mm, 10 mm and 20 mm) and diameter markings (AE, BF, CG, DH) all generated by Auto CAD. Figure 2 The end view of the tip of the Olympus BF Type 3160 bronchoscope displaying the "off set" lens and lights and the geometric centre. Magnification was calculated by repeatedly measuring the image diameters AE, BF, CG, DH across the 4 concentric circles (Fig.  1 ) at distances of 100, 80, 60, 40, 30, 25, 20, 15, 10, 5 and 3 mm and then dividing these measurements by the corresponding value of the object. These magnification measurements were repeated in 3 separate experiments and the mean value for all of the diameters of that particular circle at that particular distance was taken as the final magnification for that circle at that distance. Between the distances of 100 mm and 40 mm the calculations of the inner circle were incomplete or impossible because of the effects of the light spot obscuring the object (Fig.  3a ). Similarly as the lens approached very close to the object (5 mm to 3 mm) the outer circles became incomplete or outside the field of view (Fig.  3b ). Figure 3 Effects of distance from object on the image appearance within the Field of View (FOV) and Light intensity obscuring parts of the image. Note the barrel appearance of the graph paper at the periphery in image "A" while in image "C" these effects are clearly offset or asymmetrical. Geometrical distortion was defined as the radial length ratios from each interlocking circle with radii A taken as the denominator for all subsequent radial measurements within the outer circle and then other elements of radius A for the other circles. The uniformity of the ratios was then tested in quadrant or sectors: a sector or quadrant being an area defined in accordance with mathematical convention[ 17 ] whereby sector 1 is the NNE sector and sector 2 is NNW continuing in a anticlockwise direction for sectors 3 and 4. The comparisons were as follows: sector 1 with sector 3; sector 2 with sector 4 or the diagonal sectors with their respective opposites. This provided an understanding of the homogeneity of the distortion profile or geometrical distortion and also gives reference to curvilinear distortion. The changes in magnification across the field of view was further defined as the differences in calculated measurements for a known distance of 2 mm across the field of view at a fixed distance (15 mm) from the object. These measurements were made in the horizontal plane. As with the magnification calculations, the mean distortion value from the entire set of 3 experiments was taken as the defined distortion at the particular distance from which the measurements were made. All of the aforementioned experiments were then repeated on 3 separate Olympus BF Type 3C160 bronchoscopes. The experiments were performed separately with the central geometrical axis of the bronchoscope and then the optic axis of the bronchoscope (Fig.  2 ) aligned with the centre point of the stage and object. Statistics Magnification and distortion were expressed as mean values and comparisons between geometric and optical axis measurements were assessed by the Student's t test. A repeat measures ANOVA was used to assess the effects of distance, circle and sectorial effects. The reliability of the repeated measurements of magnification between tests and between bronchoscopes was assessed by intra-class correlation. Data storage and statistical calculations were performed on SPSS for MAC version11 (SPSS Inc., Chicago, Il, USA).
Methods
Equipment A flexible bronchoscope (Olympus BF Type 3C160, Olympus, Tokyo, Japan) and light source (Olympus Evis Exera CLV-160, Olympus, Tokyo, Japan) and processor (Olympus Evis Exera CV-160, Olympus, Tokyo, Japan) were connected to a TV monitor (Sony HR Trinitron, Sony Corporation, Shinagawa-ku, Tokyo, Japan) and a colour video printer (Sony Mavigraph, Sony Corporation, Shinagawa-ku, Tokyo, Japan) as supplied by the Olympus company. The image signals from the Evis Exera CV-160 were co-recorded by a digital camera (Sony Mini DV Digital Handycam, Sony Corporation, Shinagawa-ku, Tokyo, Japan). These digital video images were viewed and stored as uncompressed 640 × 480 pixel, millions of colours as TIFF files. These images were then analysed by an image processing program (Image J, Wayne Rasband, National Institute of Health, USA) and a computer (MAC Power Book G4. Apple Inc,, Cupertino, Ca., USA).
Equipment
A flexible bronchoscope (Olympus BF Type 3C160, Olympus, Tokyo, Japan) and light source (Olympus Evis Exera CLV-160, Olympus, Tokyo, Japan) and processor (Olympus Evis Exera CV-160, Olympus, Tokyo, Japan) were connected to a TV monitor (Sony HR Trinitron, Sony Corporation, Shinagawa-ku, Tokyo, Japan) and a colour video printer (Sony Mavigraph, Sony Corporation, Shinagawa-ku, Tokyo, Japan) as supplied by the Olympus company. The image signals from the Evis Exera CV-160 were co-recorded by a digital camera (Sony Mini DV Digital Handycam, Sony Corporation, Shinagawa-ku, Tokyo, Japan). These digital video images were viewed and stored as uncompressed 640 × 480 pixel, millions of colours as TIFF files. These images were then analysed by an image processing program (Image J, Wayne Rasband, National Institute of Health, USA) and a computer (MAC Power Book G4. Apple Inc,, Cupertino, Ca., USA).Measurement of Magnification and Distortion A precisely measured object consisting of 4 concentric circles with emanating radii on 1 mm × 1 mm graph paper was created and drawn to precision using design software (Auto CAD, Autodesk, San Rafael, Ca, USA) (Fig  1 ). These circles were 2, 6, 10 and 20 mm diameter respectively. A precision made device that fixed the hand piece and supported the length of the bronchoscope so that the central or geometric axis of the bronchoscope (Fig.  2 ) would align with the centre point of a moveable screen was engineered by Queensland Radium Institute (QRI, Brisbane, Australia) engineering. The device's moveable stage allowed the object to be positioned over a range of distances from 100 mm to 3 mm without moving the scope itself. The measured distances were verified with electronic callipers to a degree of accuracy of 0.02 mm. The calibration process for calculation of magnification and distortion was performed at the distance of 100 mm, the point at which the object to image ratio was 1. All subsequent ratios were therefore larger than the calibration value and represented the magnification of the object. Figure 1 Photographic Object: A square of graph paper 3 cms × 3 cms with 1 mm × 1 mm units and concentric circles of varying diameter (2 mm, 6 mm, 10 mm and 20 mm) and diameter markings (AE, BF, CG, DH) all generated by Auto CAD. Figure 2 The end view of the tip of the Olympus BF Type 3160 bronchoscope displaying the "off set" lens and lights and the geometric centre. Magnification was calculated by repeatedly measuring the image diameters AE, BF, CG, DH across the 4 concentric circles (Fig.  1 ) at distances of 100, 80, 60, 40, 30, 25, 20, 15, 10, 5 and 3 mm and then dividing these measurements by the corresponding value of the object. These magnification measurements were repeated in 3 separate experiments and the mean value for all of the diameters of that particular circle at that particular distance was taken as the final magnification for that circle at that distance. Between the distances of 100 mm and 40 mm the calculations of the inner circle were incomplete or impossible because of the effects of the light spot obscuring the object (Fig.  3a ). Similarly as the lens approached very close to the object (5 mm to 3 mm) the outer circles became incomplete or outside the field of view (Fig.  3b ). Figure 3 Effects of distance from object on the image appearance within the Field of View (FOV) and Light intensity obscuring parts of the image. Note the barrel appearance of the graph paper at the periphery in image "A" while in image "C" these effects are clearly offset or asymmetrical. Geometrical distortion was defined as the radial length ratios from each interlocking circle with radii A taken as the denominator for all subsequent radial measurements within the outer circle and then other elements of radius A for the other circles. The uniformity of the ratios was then tested in quadrant or sectors: a sector or quadrant being an area defined in accordance with mathematical convention[ 17 ] whereby sector 1 is the NNE sector and sector 2 is NNW continuing in a anticlockwise direction for sectors 3 and 4. The comparisons were as follows: sector 1 with sector 3; sector 2 with sector 4 or the diagonal sectors with their respective opposites. This provided an understanding of the homogeneity of the distortion profile or geometrical distortion and also gives reference to curvilinear distortion. The changes in magnification across the field of view was further defined as the differences in calculated measurements for a known distance of 2 mm across the field of view at a fixed distance (15 mm) from the object. These measurements were made in the horizontal plane. As with the magnification calculations, the mean distortion value from the entire set of 3 experiments was taken as the defined distortion at the particular distance from which the measurements were made. All of the aforementioned experiments were then repeated on 3 separate Olympus BF Type 3C160 bronchoscopes. The experiments were performed separately with the central geometrical axis of the bronchoscope and then the optic axis of the bronchoscope (Fig.  2 ) aligned with the centre point of the stage and object.
Measurement of Magnification and Distortion
A precisely measured object consisting of 4 concentric circles with emanating radii on 1 mm × 1 mm graph paper was created and drawn to precision using design software (Auto CAD, Autodesk, San Rafael, Ca, USA) (Fig  1 ). These circles were 2, 6, 10 and 20 mm diameter respectively. A precision made device that fixed the hand piece and supported the length of the bronchoscope so that the central or geometric axis of the bronchoscope (Fig.  2 ) would align with the centre point of a moveable screen was engineered by Queensland Radium Institute (QRI, Brisbane, Australia) engineering. The device's moveable stage allowed the object to be positioned over a range of distances from 100 mm to 3 mm without moving the scope itself. The measured distances were verified with electronic callipers to a degree of accuracy of 0.02 mm. The calibration process for calculation of magnification and distortion was performed at the distance of 100 mm, the point at which the object to image ratio was 1. All subsequent ratios were therefore larger than the calibration value and represented the magnification of the object.Magnification was calculated by repeatedly measuring the image diameters AE, BF, CG, DH across the 4 concentric circles (Fig.  1 ) at distances of 100, 80, 60, 40, 30, 25, 20, 15, 10, 5 and 3 mm and then dividing these measurements by the corresponding value of the object. These magnification measurements were repeated in 3 separate experiments and the mean value for all of the diameters of that particular circle at that particular distance was taken as the final magnification for that circle at that distance. Between the distances of 100 mm and 40 mm the calculations of the inner circle were incomplete or impossible because of the effects of the light spot obscuring the object (Fig.  3a ). Similarly as the lens approached very close to the object (5 mm to 3 mm) the outer circles became incomplete or outside the field of view (Fig.  3b ).Geometrical distortion was defined as the radial length ratios from each interlocking circle with radii A taken as the denominator for all subsequent radial measurements within the outer circle and then other elements of radius A for the other circles. The uniformity of the ratios was then tested in quadrant or sectors: a sector or quadrant being an area defined in accordance with mathematical convention[ 17 ] whereby sector 1 is the NNE sector and sector 2 is NNW continuing in a anticlockwise direction for sectors 3 and 4. The comparisons were as follows: sector 1 with sector 3; sector 2 with sector 4 or the diagonal sectors with their respective opposites. This provided an understanding of the homogeneity of the distortion profile or geometrical distortion and also gives reference to curvilinear distortion.The changes in magnification across the field of view was further defined as the differences in calculated measurements for a known distance of 2 mm across the field of view at a fixed distance (15 mm) from the object. These measurements were made in the horizontal plane. As with the magnification calculations, the mean distortion value from the entire set of 3 experiments was taken as the defined distortion at the particular distance from which the measurements were made. All of the aforementioned experiments were then repeated on 3 separate Olympus BF Type 3C160 bronchoscopes. The experiments were performed separately with the central geometrical axis of the bronchoscope and then the optic axis of the bronchoscope (Fig.  2 ) aligned with the centre point of the stage and object.Statistics Magnification and distortion were expressed as mean values and comparisons between geometric and optical axis measurements were assessed by the Student's t test. A repeat measures ANOVA was used to assess the effects of distance, circle and sectorial effects. The reliability of the repeated measurements of magnification between tests and between bronchoscopes was assessed by intra-class correlation. Data storage and statistical calculations were performed on SPSS for MAC version11 (SPSS Inc., Chicago, Il, USA).
Statistics
Magnification and distortion were expressed as mean values and comparisons between geometric and optical axis measurements were assessed by the Student's t test. A repeat measures ANOVA was used to assess the effects of distance, circle and sectorial effects. The reliability of the repeated measurements of magnification between tests and between bronchoscopes was assessed by intra-class correlation. Data storage and statistical calculations were performed on SPSS for MAC version11 (SPSS Inc., Chicago, Il, USA).Results The mean linear magnification for the bronchoscopes aligned along the central geometrical axis of the bronchoscope over the range of the depth of field from 100 mm to 3 mm is shown in  Additional file 1 . The magnification progressively increased in a linear fashion between 100 and 10 mm from the object and then exponentially increased to 40 times between the distances of 10 mm and 3 mm from the object. The magnification factor was approximately ×10 at 10 mm and ×40 at 3 mm from the object. The graphic representation of these values as tightly fitting linear becoming exponential curves is displayed in Figure  4 . The goodness of fit (R 2  value) for each of the curves for circles A,B,C,D was 0.999, 0.999, 0.999 and 0.999 respectively. When the bronchoscope was aligned to the object through the optical axis, the magnification was reduced generally but by as much as 22% at 5 mm and 14.5% at 10 mm from the object ( Additional file 2 ). Figure 4 Effects of position within the Field of View: Magnification changes from 40 mm to 3 mm from the object displaying the variable exponential changes in magnification close to the object. The mean intra-class correlation alpha level for the repeated measurement of magnification ranged from 0.9369 (95%CI: 0.6167 to 0.9878) to 0.9811 (95%CI: 0.8827 to 1.000). These intraclass correlation data indicate and support the goodness of fit of the regression curves. The variability in magnification measurement between the bronchoscopes was extremely small and there are virtually no differences between the bronchoscopes (Table  1 ). The reliability coefficient average alpha value for the measurements from 3 separate bronchoscopes assessed at 10 mm was 0.9996 (95%CI: 0.9991 to 0.9999). Table 1 Inter-scope comparison of magnification with optical axis aligned. Bronchoscope No. Distance mm Circle A Circle B Circle C Circle D 324 30 3.0938 3.1601 3.2913 292 30 3.0984 3.1963 3.3258 039 30 3.0820 3.2083 3.3191 324 15 5.5356 6.2137 6.4443 6.4918 292 15 5.5016 6.1527 6.3062 6.3832 039 15 5.4997 6.1107 6.6364 6.4358 324 10 8.9428 9.5024 9.6755 292 10 8.5663 9.0650 9.3453 039 10 8.5663 9.0649 9.3449 324 5 17.6819 19.8996 292 5 15.9314 17.0974 039 5 15.6890 16.7272 324 3 32.4274 292 3 26.1051 039 3 24.7775 The across field magnification was greatest in the centre of the field and least at the periphery with some 38.5% reduction in magnification across a 20 mm diameter object but only 15.4% across an object of 6 mm diameter (Figure  5 ). The overall distortion including geometric distortion for the bronchoscopes aligned along the central axis ranged from near zero at 40 mm, 5% at 5 mm but at 3 mm it had risen to 30% (Figure  6 ). When the object very closely approximated the optical axis in alignment (object centre is within 2 mm of the lens's optical axis), the overall magnification factors changed (see  additional file 2 ) but importantly this value of distortion at 3 mm from the object was markedly reduced to 5%. Distortion was significantly different in different quadrants when the scopes were aligned along their central geometrical axes to the object. Figure 5 Across lens magnification: the near linear changes in magnification across the horizontal plane from the centre to periphery of the lens. Figure 6 Mean central distortion ± 95% CI for the central or geometrical axis aligned bronchoscope. The appearance of the curvilinear distortion is shown in Figure  3  and clearly displays barrel distortion. The measurements show that curvilinear distortion was different for the different parts of the field of view. In particular, the magnification at the centre of the field of view at any distance was different to the periphery (Figure  5 ). These differences were not evenly distributed across the field of view, however the differences between quadrants were extremely small. A univariate analysis found significant effects for ring, distance and sector analysis. However the three factor repeat measures ANOVA analysis revealed no significant differences between measures by sector (adjusted p-value using Box's conservative test = 0.13). When the data was stratified by distance, all 8 p-values were not significant (0.13 to 0.31), indicating that a mild effect by sector may exist.
Results
The mean linear magnification for the bronchoscopes aligned along the central geometrical axis of the bronchoscope over the range of the depth of field from 100 mm to 3 mm is shown in  Additional file 1 . The magnification progressively increased in a linear fashion between 100 and 10 mm from the object and then exponentially increased to 40 times between the distances of 10 mm and 3 mm from the object. The magnification factor was approximately ×10 at 10 mm and ×40 at 3 mm from the object. The graphic representation of these values as tightly fitting linear becoming exponential curves is displayed in Figure  4 . The goodness of fit (R 2  value) for each of the curves for circles A,B,C,D was 0.999, 0.999, 0.999 and 0.999 respectively. When the bronchoscope was aligned to the object through the optical axis, the magnification was reduced generally but by as much as 22% at 5 mm and 14.5% at 10 mm from the object ( Additional file 2 ).The mean intra-class correlation alpha level for the repeated measurement of magnification ranged from 0.9369 (95%CI: 0.6167 to 0.9878) to 0.9811 (95%CI: 0.8827 to 1.000). These intraclass correlation data indicate and support the goodness of fit of the regression curves. The variability in magnification measurement between the bronchoscopes was extremely small and there are virtually no differences between the bronchoscopes (Table  1 ). The reliability coefficient average alpha value for the measurements from 3 separate bronchoscopes assessed at 10 mm was 0.9996 (95%CI: 0.9991 to 0.9999).Inter-scope comparison of magnification with optical axis aligned.Bronchoscope No.Distance mmCircle ACircle BCircle CCircle DThe across field magnification was greatest in the centre of the field and least at the periphery with some 38.5% reduction in magnification across a 20 mm diameter object but only 15.4% across an object of 6 mm diameter (Figure  5 ). The overall distortion including geometric distortion for the bronchoscopes aligned along the central axis ranged from near zero at 40 mm, 5% at 5 mm but at 3 mm it had risen to 30% (Figure  6 ). When the object very closely approximated the optical axis in alignment (object centre is within 2 mm of the lens's optical axis), the overall magnification factors changed (see  additional file 2 ) but importantly this value of distortion at 3 mm from the object was markedly reduced to 5%. Distortion was significantly different in different quadrants when the scopes were aligned along their central geometrical axes to the object.The appearance of the curvilinear distortion is shown in Figure  3  and clearly displays barrel distortion. The measurements show that curvilinear distortion was different for the different parts of the field of view. In particular, the magnification at the centre of the field of view at any distance was different to the periphery (Figure  5 ). These differences were not evenly distributed across the field of view, however the differences between quadrants were extremely small. A univariate analysis found significant effects for ring, distance and sector analysis. However the three factor repeat measures ANOVA analysis revealed no significant differences between measures by sector (adjusted p-value using Box's conservative test = 0.13). When the data was stratified by distance, all 8 p-values were not significant (0.13 to 0.31), indicating that a mild effect by sector may exist.Discussion This is the first reported study detailing systematically the magnification and distortion factors that surround the optic properties of a commonly used pediatric video-bronchoscope. The magnification progressively increases in a linear fashion over the distances of 100 mm to 10 mm with changes from 1 to near 10 fold magnification. However below 10 mm, the magnification changes exponentially thus making appreciation of the actual or real size of the object very difficult even when the distance from the object is known [ 3 , 5 , 6 ]. This study also shows that the magnification of the instrument changes is accordance with the axis of orientation of the bronchoscope to the object. These data indicate that the optimal operating distance is between 40 mm and 10 mm where the mean magnification is linear and is 3 to 9.5 fold and the distortion of any form can be under 5%. However it also means that it is important for the bronchoscopist to maintain a "perspective of operating distance" or distance from the object when judgements of size are to be made. This study has also shown that the Image J and BTV programs and MAC power book G4 can be readily interfaced with Olympus BF Type 3C160 to produce an objective measurement package. In addition this system could be readily adapted to most image acquisition systems and varieties of flexible bronchoscopes types (FVB and fibre optic) that must be in clinical use around the world. With respect to distortion, this study has shown that geometric distortion can result with very significant errors in size perception with up to 30 percent distortion occurring if the lens is placed very close to the object (<5 mm) and the object is not aligned through the optical axis. This could be corrected by movement of the object closer to the line of the optical axis of the lens. However there are no markers on the bronchoscope to indicate that this position has been gained. At close proximity to this point there is separation of the light beams, however while the use of this is possible in laboratory settings, it is not currently possible in the clinical context where there are differences in reflectance and absorption of light. The second issue is that barrel distortion is generally regarded as homogeneous and independent of working distance however when the lens is offset as it is in this type of instrument it cannot be, given the differences between the geometrical and optical axes of the bronchoscope. In the clinical context these issues indicate that clinicians must be aware that their judgements always contain "distortion effects" but particularly when working very close to the object eventhough the image appears clear and is centred on the screen. The limitations of this study are the fact that the object positioning could only be moved with micrometer precision in the longitudinal plane. However an instrument that allowed for lateral movement of the object with micrometer precision may have produced less distortion but in the clinical context such precision could only ever be transient and thus these methods have allowed for a greater appreciation of the extent and complexity of distortion. Even though computer based systems have been used to correct for some of the elements of distortion[ 3 , 5 , 6 ] none exist in routine use within the current hardware of the bronchoscopes themselves. In those that have been described [ 5 ], it is unclear as to what type of distortion has been corrected. These authors have aligned their image centre or Field of View (FOV) as the centre for their measurements. However as shown in this study, correction for the offset position of the lens is important to any real measurement when the object is closer than 5 mm. If this is not done, then correction formulations will overestimate the levels of distortion in some instances, as there would be a high likelihood that the objects of view would pass through all axes of orientation during an in vivo procedure. Despite these arguments, the overall distortion of any type is extremely low and in the clinical context these values are highly acceptable as far as measurements are concerned. Also it is unlikely that an object will be viewed at this distance for any period of time given the "blurring effects" of the distortion. However during passage of the bronchoscope across lesions, clearly such transients in magnification and distortion could be misleading. The clinical relevance of this work may not be obvious. However, we argue that it has a number of important clinical applications and that all bronchoscopists should be cognisant of these factors, which may influence their judgement of the size of lesions. Firstly, the distance of the tip of the scope to the lesions being assessed must be measured and not approximated by judgement as distances under 5 mm may result in very considerable differences in magnification and thus the estimates of size or even presence or absence of a lesion. The most obvious example of this is in assessments of a curvaceous left main stem bronchus that may initially appear as malacia but appears to become "normal" as it is viewed at a closer distance. Indeed in defining malacia a viewing or operating distance must be stated otherwise these perspective difficulties will prevail and comparative statements and judgements become meaningless. Another example occurs when assessing malacia or airway cross sectional area changes across the respiratory cycle. In that scenario the movement of the object is away from the lens during inspiration making the image relatively smaller than is real for the increase in lung volume. These optic effects combined with the venturi effects from the bronchoscope itself on reducing intraluminal pressure again compound the issue and reduce the image size or its relative changes. Bronchoscopists need to be aware of these apparent paradoxical effects, that the lumen is greatest at the end of expiration. Indeed at this point in time and until the distance of airway movement can be measured in vivo, measurements can only be made precisely at one point in the respiratory cycle, and that generally is the end expiratory point. If end inspiration is used there is likely to be intrusion of the mucosa into the field of view during the subsequent expiration. The most recent published example of most of these effects can be seen in the images provided in that paper by Okasaki et al [ 18 ] where the instrumentation magnification is not known, the measurements are not calibrated at a defined time in the respiratory cycle, the viewing distance is not described and there is clearly image change across the induced respiratory cycle. Secondly, paradoxical concepts also apply to the use of the flexible bronchoscope in assessment and or removal of foreign bodies situated peripherally in the airways. When dealing with peripheral or markedly angulated bronchial branches it is not always possible to position the image in the centre of the screen. Here estimates of size may be misconstrued by the interactions of variable magnification across the lens, curvilinear distortion and potentially geometric distortion. These effects and the "iceberg effects" of the presented foreign body size usually mean that the foreign body appears smaller than it really is and the inexperienced bronchoscopists might tend to dismiss the object as trivial or inconsequential. To the contrary attempts to remove it should be maximized. Finally, in terms of research, defining the position of the bronchoscope in terms of the lesion being assessed and photographed is vital if realistic comparisons are to be made across time or between groups. In this regard techniques that allow for distance and lesions measurement and assessment need to be developed and integrated into routine clinical use. Using our technique described in this paper, we are quantifying airway size in a variety of airway lesions (eg tracheobronchomalacia) associated with significant respiratory morbidity. The fact that performance of each bronchoscope was remarkably similar in terms of magnification and distortion measurements obviously reflects company's production quality. In a clinical session where a number of bronchoscopes might be used and in research where inter-group comparisons might be desired, this information suggests that a significant level of confidence can be maintained in perception terms for the bronchoscopists. This does not negate the need for individual bronchoscope calibration and for objective and accurate measurements in bronchoscopic work. Detailed data from the Olympus Company was not available for comparison; however our own validation experiments show these data to be correct and accurate. Despite the latter, as there are now many instruments available to the clinician, we suggest that companies and manufacturing regulators make readily available the magnification and distortion characteristics of each instrument type or size so that more effective clinical appraisals can occur. Although this study has shown that the Olympus BF Type 3C160 video-bronchoscopes produce remarkably consistent magnification across the working ranges of 100 mm to 3 mm from the object, an understanding of the influence of distance on magnification and distortion of the image obtained by a flexible bronchoscope is an essential step in the development of an invivo technique of measuring airway sizes. We have provided graphic appreciation of these effects and the importance of optical versus geometric axis orientation. The optimal working distances for this bronchoscope are between 40 mm and 10 mm from the object. The study also provides reasonable working magnification factors for this type of bronchoscope and as such could allow for a better appreciation of real or actual airway sizes.
Discussion
This is the first reported study detailing systematically the magnification and distortion factors that surround the optic properties of a commonly used pediatric video-bronchoscope. The magnification progressively increases in a linear fashion over the distances of 100 mm to 10 mm with changes from 1 to near 10 fold magnification. However below 10 mm, the magnification changes exponentially thus making appreciation of the actual or real size of the object very difficult even when the distance from the object is known [ 3 , 5 , 6 ]. This study also shows that the magnification of the instrument changes is accordance with the axis of orientation of the bronchoscope to the object. These data indicate that the optimal operating distance is between 40 mm and 10 mm where the mean magnification is linear and is 3 to 9.5 fold and the distortion of any form can be under 5%. However it also means that it is important for the bronchoscopist to maintain a "perspective of operating distance" or distance from the object when judgements of size are to be made. This study has also shown that the Image J and BTV programs and MAC power book G4 can be readily interfaced with Olympus BF Type 3C160 to produce an objective measurement package. In addition this system could be readily adapted to most image acquisition systems and varieties of flexible bronchoscopes types (FVB and fibre optic) that must be in clinical use around the world.With respect to distortion, this study has shown that geometric distortion can result with very significant errors in size perception with up to 30 percent distortion occurring if the lens is placed very close to the object (<5 mm) and the object is not aligned through the optical axis. This could be corrected by movement of the object closer to the line of the optical axis of the lens. However there are no markers on the bronchoscope to indicate that this position has been gained. At close proximity to this point there is separation of the light beams, however while the use of this is possible in laboratory settings, it is not currently possible in the clinical context where there are differences in reflectance and absorption of light. The second issue is that barrel distortion is generally regarded as homogeneous and independent of working distance however when the lens is offset as it is in this type of instrument it cannot be, given the differences between the geometrical and optical axes of the bronchoscope. In the clinical context these issues indicate that clinicians must be aware that their judgements always contain "distortion effects" but particularly when working very close to the object eventhough the image appears clear and is centred on the screen.The limitations of this study are the fact that the object positioning could only be moved with micrometer precision in the longitudinal plane. However an instrument that allowed for lateral movement of the object with micrometer precision may have produced less distortion but in the clinical context such precision could only ever be transient and thus these methods have allowed for a greater appreciation of the extent and complexity of distortion. Even though computer based systems have been used to correct for some of the elements of distortion[ 3 , 5 , 6 ] none exist in routine use within the current hardware of the bronchoscopes themselves. In those that have been described [ 5 ], it is unclear as to what type of distortion has been corrected. These authors have aligned their image centre or Field of View (FOV) as the centre for their measurements. However as shown in this study, correction for the offset position of the lens is important to any real measurement when the object is closer than 5 mm. If this is not done, then correction formulations will overestimate the levels of distortion in some instances, as there would be a high likelihood that the objects of view would pass through all axes of orientation during an in vivo procedure. Despite these arguments, the overall distortion of any type is extremely low and in the clinical context these values are highly acceptable as far as measurements are concerned. Also it is unlikely that an object will be viewed at this distance for any period of time given the "blurring effects" of the distortion. However during passage of the bronchoscope across lesions, clearly such transients in magnification and distortion could be misleading.The clinical relevance of this work may not be obvious. However, we argue that it has a number of important clinical applications and that all bronchoscopists should be cognisant of these factors, which may influence their judgement of the size of lesions. Firstly, the distance of the tip of the scope to the lesions being assessed must be measured and not approximated by judgement as distances under 5 mm may result in very considerable differences in magnification and thus the estimates of size or even presence or absence of a lesion. The most obvious example of this is in assessments of a curvaceous left main stem bronchus that may initially appear as malacia but appears to become "normal" as it is viewed at a closer distance. Indeed in defining malacia a viewing or operating distance must be stated otherwise these perspective difficulties will prevail and comparative statements and judgements become meaningless. Another example occurs when assessing malacia or airway cross sectional area changes across the respiratory cycle. In that scenario the movement of the object is away from the lens during inspiration making the image relatively smaller than is real for the increase in lung volume. These optic effects combined with the venturi effects from the bronchoscope itself on reducing intraluminal pressure again compound the issue and reduce the image size or its relative changes. Bronchoscopists need to be aware of these apparent paradoxical effects, that the lumen is greatest at the end of expiration. Indeed at this point in time and until the distance of airway movement can be measured in vivo, measurements can only be made precisely at one point in the respiratory cycle, and that generally is the end expiratory point. If end inspiration is used there is likely to be intrusion of the mucosa into the field of view during the subsequent expiration. The most recent published example of most of these effects can be seen in the images provided in that paper by Okasaki et al [ 18 ] where the instrumentation magnification is not known, the measurements are not calibrated at a defined time in the respiratory cycle, the viewing distance is not described and there is clearly image change across the induced respiratory cycle.Secondly, paradoxical concepts also apply to the use of the flexible bronchoscope in assessment and or removal of foreign bodies situated peripherally in the airways. When dealing with peripheral or markedly angulated bronchial branches it is not always possible to position the image in the centre of the screen. Here estimates of size may be misconstrued by the interactions of variable magnification across the lens, curvilinear distortion and potentially geometric distortion. These effects and the "iceberg effects" of the presented foreign body size usually mean that the foreign body appears smaller than it really is and the inexperienced bronchoscopists might tend to dismiss the object as trivial or inconsequential. To the contrary attempts to remove it should be maximized. Finally, in terms of research, defining the position of the bronchoscope in terms of the lesion being assessed and photographed is vital if realistic comparisons are to be made across time or between groups. In this regard techniques that allow for distance and lesions measurement and assessment need to be developed and integrated into routine clinical use. Using our technique described in this paper, we are quantifying airway size in a variety of airway lesions (eg tracheobronchomalacia) associated with significant respiratory morbidity.The fact that performance of each bronchoscope was remarkably similar in terms of magnification and distortion measurements obviously reflects company's production quality. In a clinical session where a number of bronchoscopes might be used and in research where inter-group comparisons might be desired, this information suggests that a significant level of confidence can be maintained in perception terms for the bronchoscopists. This does not negate the need for individual bronchoscope calibration and for objective and accurate measurements in bronchoscopic work. Detailed data from the Olympus Company was not available for comparison; however our own validation experiments show these data to be correct and accurate. Despite the latter, as there are now many instruments available to the clinician, we suggest that companies and manufacturing regulators make readily available the magnification and distortion characteristics of each instrument type or size so that more effective clinical appraisals can occur.Although this study has shown that the Olympus BF Type 3C160 video-bronchoscopes produce remarkably consistent magnification across the working ranges of 100 mm to 3 mm from the object, an understanding of the influence of distance on magnification and distortion of the image obtained by a flexible bronchoscope is an essential step in the development of an invivo technique of measuring airway sizes. We have provided graphic appreciation of these effects and the importance of optical versus geometric axis orientation. The optimal working distances for this bronchoscope are between 40 mm and 10 mm from the object. The study also provides reasonable working magnification factors for this type of bronchoscope and as such could allow for a better appreciation of real or actual airway sizes.Supplementary Material Additional File 1 Mean magnification and the mean whole of field magnification at defined distances. Click here for file Additional File 2 Comparison of bronchoscope axis and optical axis aligned magnification measurements. Click here for file
Supplementary Material
Additional File 1
Mean magnification and the mean whole of field magnification at defined distances.Click here for fileAdditional File 2
Comparison of bronchoscope axis and optical axis aligned magnification measurements.Click here for file


After apprenticing at her mother's side for some eight years—the first three clinging to her body—an orangutan is ready to make her own way in the forest canopy. The only great ape specializing in arboreal living, orangutans forage the treetops mostly for fruit, nuts, insects, leaves, and tree bark. They can recognize hundreds of species of edible fruit from trees and woody climbers and remember their location and fruiting season. Malay legend says orangutans (a variation on the Malay trope for “man of the woods”) derived from humans who sought refuge from their species in the wilds of the forest. Today, with the last orangutan refuges shrinking drastically, the man of the woods has nowhere else to go.Hundreds of thousands of orangutans once ranged throughout southeast Asia. Now just two orangutan species inhabit just two countries: Indonesia (Kalimantan, the southern part of Borneo and Sumatra Island) and Malaysia (Sabah and Sarawak, in northern Borneo). The Sumatran orangutan is listed as critically endangered; the Bornean, endangered. In Indonesian Borneo and Sumatra, logging operations clear an estimated 5 to 6 million forest acres a year, leaving the apes stranded in isolated stands of trees and the normally fire-resistant rainforest at sudden risk. Another force driving orangutan extinction in Indonesia is the poaching and illegal killing (mothers do not give up their babies without a fight) that secures orangutan babies for the exotic pet trade. In Sabah, Malaysia, the primary threat comes from clearing the forest for agriculture.Conservation efforts depend, among other things, on having reliable data on population size, density, and distribution, but estimates of orangutan numbers in Sabah—which range from 2,000 to 20,000—are outdated. In a new study, Marc Ancrenaz and colleagues report an innovative method of directly estimating orangutan numbers from the number of nests detected during aerial surveys. (Orangutans are tough to spot directly, so researchers count the nests they sleep in at night.) Their survey, which covered the entire orangutan range throughout Sabah, estimates a total population of 11,000 orangutans—a drop of 35% in the past 20 years, based on a 1988 World Wildlife Federation report.Counting orangutans from the ground can be very time-consuming, difficult work, especially when faced with the hip-deep muck and steep slopes of the rainforest floor. Though helicopters obviously cover greater distance and more remote territory than is possible by foot, they're generally used to survey animals in more open landscapes. By using ground survey data to refine their aerial survey results, Ancrenaz and colleagues could directly assess the distribution and size of orangutan populations throughout Sabah. (Sabah covers roughly 72,000 square kilometers.)Over the course of two years, ground surveys—requiring 1,100 hours of field work—and aerial surveys—requiring just 72 hours—were conducted throughout all the major forests of Sabah. Commercial logging occurs in about 76% of all Sabah forests in commercial forest reserves. During the overflights, information was recorded on altitude, forest type, forest disturbance (on a scale from none to active exploitation), and signs of human activity.The authors attribute the 35% decline in Sabah orangutan numbers primarily to habitat loss from agricultural development. The surveys revealed that lowland forests harbored the greatest density of nests and orangutans, with the densest populations found in several highly disturbed, fragmented forests along newly created palm oil plantations. These high orangutan densities could reflect an influx of refugees from recently destroyed forest habitat into areas that are still forested. In logged forests, higher population densities were found in old exploited or sustainably logged forests than in conventionally logged reserves.While the authors acknowledge the density estimates could be more precise—better measures of nest decay and construction rates are needed—their survey reveals crucial information on orangutan numbers and distribution. Most orangutans in Sabah, including those making up one of the largest unfragmented populations in Borneo, live outside protected areas, in commercially exploited forests. These results suggest that orangutans may adapt better to degraded forests than previously thought—provided illegal hunting and agricultural conversion are controlled.More field research will help quantify the impacts of human activity—from logging to stealing babies—on great ape ecology and survival, and determine whether exploited forests can support conservation. It may be, for example, that integrating agricultural fields with forested corridors could sustain orangutan populations over the long term. With time of the essence, these aerial surveys will speed that work, and help sustain orangutans' refuge in the treetops, above their human relatives.


Is biodiversity decreasing or is it being replaced by a splendid profusion of microbes -- and does this matter?

There is an old Chinese curse: ‘May you live in interesting times.’ According to those who know about such things, we live in a momentous time, the time of the Sixth Mass Extinction! But most of us do not feel at all cursed. Because, in fact, the Sixth is quite different to the previous Big Five—no-one would notice this one if we were not repeatedly reminded of it by ecologists. Previous mass extinctions were not so bashful, so discreet. The fossil record reveals the disappearance of pollen during previous ones, replaced by an abundance of fungus spores, telling us of a world of devastated forests rotting away. The earliest sediments after the mass extinction that did away with the dinosaurs are barren of fossils: so it is not just that species were going extinct, conditions for life itself were bad. Not only did species diversity drop, the abundance of life did as well.But conditions for life itself have never been better than today. In the history of the planet, there has never been anything as productive of life as a wheat field in Kansas. It may not have a large diversity of species, but that is a different matter. In fact, one of the reasons for the ongoing loss of plant diversity from grasslands is the very reason the wheat field is so productive—fertilisation. We are pouring nitrogen fertiliser into the environment and, through the wellstudied ‘paradox of enrichment’, this reduces species diversity while increasing actual biomass. Now, there is no question that if current trends of habitat alteration and climate change continue then we will ultimately lose large numbers of species—diversity will drop—but this does not necessarily translate into a loss of abundance of life, and that is a big difference between now and previous mass extinctions. Looking at specific groups of organisms tells the same story. So, for example, many island bird species are threatened, like the kagu of New Caledonia, but British seabird populations, like puffins, are booming. Worldwide amphibian diversity is threatened, but cane toads are a pest in Australia. Introduced species pose a threat to diversity—the ‘McDonald-isation’ of nature—precisely because they achieve enormous abundances.Actually, all six mass extinctions may have one very important thing in common: from the point of view of the vast bulk of life on the planet they are probably not mass extinctions at all. By any criterion—number of individuals or total biomass—the vast majority of life on earth is invisible—microbial. So, for example, at least 10% of the living biomass on earth consists of bacteria living deep in the oceans' sediments: it would take more than an asteroid impact to disturb them. And microbial life is extraordinarily robust: microbes can be found living happily in pressurised water hotter than your boiling kettle, in concentrated acid, and in rock, and their spores can survive for years in the rigours of outer space.In talks and lectures, the renowned oceanographer and paleontologist Jeremy Jackson paints a vivid picture of what is currently happening to coastal ecosystems, talking about a wall of slime emanating from populated areas and growing outwards inexorably towards the open oceans, replacing beloved ecologies like coral reef systems. What he means is that the visible life that we find attractive and useful—pretty fish, turtles, and so on—is being replaced by microbes in splendid profusion. It is taken completely for granted that this is disastrous. From a utilitarian point of view indeed it is disastrous, since we like eating fish and turtles, and don't like snorkling in slime. But from the point of view of life per se, again things have never been better. Life is so abundant that in some places all the oxygen in the water is completely used up. These are called ‘dead zones’, but they are no more ‘dead’ than the Dead Sea, which is actually teeming with life—just not fish. But, nonetheless, we consider what is occurring to be a disaster not just from a utilitarian point of view, but at some deeper level giving us an emotional reaction to the word ‘slime’—somehow it is just plain wrong.But this reflects nothing other than our evolutionary origins. Evolution has programmed us to be positively interested in plants and animals, our food, and to be repelled by slimes and oozes, teeming with potentially harmful microbes. These emotional responses colour our view of ecology, for example, in a way that has no parallel in other sciences: physicists do not just study particles that they find pretty. No ecologist wants to study the rich ecosystem that each of us carries around inside our gut, because evolution has programmed our brains to find bottom-related matters disgusting. I think it likely that naturalists from a different planet, silicon entities evolved under very different circumstances, would find tropical forests uninteresting (mainly primary producers with some herbivory and mutualisms) and animal guts fascinating, with their complex metabolic networks in which each node is manned by different species with wildly varying means of energy production.Our guts should be an ecological scientist's dream come true, ecological theatres that are replicated billions of times, which operate on a fast time scale and are easy to get to! (If aliens are ecologists, this would explain why they always ‘probe’ their abductees.) Many natural experiments are going on all the time as antibiotics and probiotics are administered and people find all sorts of different ways, voluntary or otherwise, to establish migration links between their gut ecologies. Microbiologists are increasingly interested in our guts from an ecological point of view but, unlike ecologists, they are used to faeces from their work in sewage plants.Two thousand years ago the Roman senator Cicero noted the creation of barren desert-like land in North Africa after the forests were felled for their timber, providing the earliest record of an ecosystem ‘service’ provided by forests—the stabilisation of soils. Other services provided by biodiversity readily come to mind, like pollination and carrion clean-up, and there may be many more. But perhaps the clearest example of an ecosystem service provided by biodiversity comes from our gut. Throughout our history, until very recently, we all had worms. In rich countries we have quite happily eradicated them from our inner ecosystems with none of the handwringing we expend on rhinos. But it is increasingly believed that the loss of worms from our internal ecology is responsible for the upsurge in inflammatory bowel disorders such as Crohn's disease and colitis. In fact, there are clinical trials underway in the United States testing the efficacy of worms as treatment for these diseases. The mechanism is clear: worms trigger one arm of the immune system which down-regulates another, inflammatory arm. Our immune system has evolved to expect a certain constellation of species in our gut: in that context, worms provide an ecosystem service of balancing the immune system.Our perception of our impact on the planet as equivalent to a mass extinction simply reflects the evolutionary prism through which we view life. Of course, we may yet live up to our own publicity and pull off something apocalyptic like a runaway greenhouse that sterilises the Earth. But it is at least as likely that the microbial world, resentful at being either ignored or exterminated, will come up with something to consign us to a footnote in the history of life when it is ultimately written by the silicon entities. The Spanish flu, SARS, and HIV have just been early experiments.


Anyone who's endured their share of childhood scrapes has probably heard some version of the motherly admonishment, “Don't pick that scab, you'll just make it worse!” It turns out, Mom was on to something. Tissue damage in humans triggers a well-characterized response marked by rapid blood clotting and a recruitment of epidermal cells to the injury. When you remove a scab, you're also removing some of the newly regenerated tissues growing underneath, thereby interfering with the healing process.Many different cell types and proteins have been linked to the repair process, but the complexity of the mammalian wound response has challenged efforts to determine their individual roles. Only the first step—the signaling cascade that promotes blood clotting—is understood at the molecular level. Since dissecting the wound response pathway at the molecular level requires an organism that lends itself to relatively easy genetic manipulations, Michael Galko and Mark Krasnow of Stanford University turned to the quintessential genetics organism,  Drosophila melanogaster , to create a novel system for studying wound healing. After stabbing fruitfly larvae with a needle to create a nonfatal puncture wound, Galko and Krasnow then analyzed significant morphological, cellular, and molecular events at various stages of healing.Drosophila melanogasterImmediately after wounding, the larvae begin to bleed, and about 15 minutes after wounding, the wound darkens and a “plug” of cellular debris forms in the wound. The plug staunches the bleeding and provides a protective layer. Within two hours the plug's outer layer forms a dark, tough scab that presumably serves as an effective barrier to further blood loss. Two or three days later, the healing process is complete.Galko and Krasnow observed the activity of epidermal cells during healing by labeling their nuclei with a fluorescent protein and staining their membranes. Soon after wounding, cells along the wound margin elongated and aligned themselves toward the wound, then fused together to form a large, multinucleate (multiple nuclei) epidermal cell surrounding the scab. Over the next six hours, these cells also spread along and through the plug, re-establishing a continuous epidermis.Since this epidermal spreading resembles that seen during a developmental stage of the fruitfly, where the process depends on the JNK signaling pathway, the authors investigated JNK signaling to shed light on the genetics and cellular events of healing. Sure enough, they found that the JNK pathway was activated during the peak hours of wound healing. Inhibiting the pathway in fly mutants—the classic approach in fly genetics—had dramatic effects on the wound-healing process. The early stages of healing—including plug and scab formation—weren't affected, but epidermal spreading to regenerate the intact epidermis was either blocked or defective. In contrast, larvae with defects in a gene required for the generation of crystal cells—a type of blood cell implicated in processes linked to scab formation—could not properly form scabs. In these scabless wounds, the JNK pathway was hyperactive, epidermal cells at the wound's margin started to spread to close the wound but often failed, and the wound did not heal. Score one for Mom.But apparently Mom wasn't totally right: As Galko and Krasnow discovered, a scab isn't always necessary. When the authors pinched larvae without puncturing the overlying cuticle, the wounds did not form scabs. However, they still saw many of the same processes at work around this “pinch” wound that they saw around the puncture wound, and the pinch wounds healed efficiently. This indicates, the authors argue, that the scab functions primarily to provide stability to the wound site and help restore tissue integrity when both the epidermis and overlying cuticle are damaged during wounding.While the stages of wound healing outlined here occur at a particular time and place, these results suggest that each stage is controlled by distinct genetic programs and signaling pathways triggered by the wound. Since many aspects of the fly wound response resemble those in mammals, it's likely that the molecular components are also shared. That makes identifying the molecular underpinnings of wound healing a high research priority. And thanks to the powerful system presented here, this task should be all the easier.