Bioblast - Recent changes [en]

Autophagy

2012-05-20T14:54:35Z

New page

AMPK

2012-05-20T14:48:56Z

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	\|mitopedia topic=Enzyme, Substrate and metabolite		\|mitopedia topic=Enzyme, Substrate and metabolite
	}}		}}
-	'''AMPK''' is a regulatory protein which acts as crucial cellular energy sensor by sensing AMP, ADP and/or Ca2+ levels in response to metabolic stresses or drug administration. AMPK can also be activated by reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). Basically, it regulates energy balance by activating catabolic pathways that generate ATP while conserving ATP by downregulating anabolic pathways. AMPK is a heterotrimeric protein (catalytic α-subunit and regulatory β- and γ-subunits). The well-known oral antidiabetic drug metformin, thiazolidinediones, resveratrol and AICAR as well as many other xenobiothics exerts their mechanism of action by activating AMPK.	+	'''AMPK''' is a regulatory protein which acts as crucial cellular energy sensor by sensing AMP, [[ADP]] and/or Ca2+ levels in response to metabolic stresses or drug administration. AMPK can also be activated by reactive oxygen species ([[ROS]]) such as hydrogen peroxide (H2O2). Basically, it regulates energy balance by activating catabolic pathways that generate ATP while conserving ATP by downregulating anabolic pathways. AMPK is a heterotrimeric protein (catalytic α-subunit and regulatory β- and γ-subunits). The well-known oral antidiabetic drug metformin, thiazolidinediones, resveratrol and AICAR as well as many other xenobiothics exerts their mechanism of action by activating AMPK.

	'''Activation'''		'''Activation'''

	Severe cellular energy stress causes a rise in AMP/ATP and ADP/ATP ratios. Upon binding of AMP and - as has recently been found - ADP to regulatory γ-subunit Thr172 is phosphorylated by upstream kinase LKB1–STRAD–MO25 complex or, alternatively, by Ca2+/calmodulin-activated protein kinase kinase, CaMKKβ. CaMKKβ, however, senses Ca2+ levels rather than changes in adenine nucleotides. Upon activation, AMPK upregulates genes involved in oxidative metabolism and oxidative stress resistance by regulating a number of transcription factors which affects the healthy lifespan. It activates catabolic pathways such as glucose uptake, glycolysis, fatty acid uptake, and fatty acid oxidation. AMPK also induces mitochondrial biogenesis, most likely by directly phosphorylating PGC1α.		Severe cellular energy stress causes a rise in AMP/ATP and ADP/ATP ratios. Upon binding of AMP and - as has recently been found - ADP to regulatory γ-subunit Thr172 is phosphorylated by upstream kinase LKB1–STRAD–MO25 complex or, alternatively, by Ca2+/calmodulin-activated protein kinase kinase, CaMKKβ. CaMKKβ, however, senses Ca2+ levels rather than changes in adenine nucleotides. Upon activation, AMPK upregulates genes involved in oxidative metabolism and oxidative stress resistance by regulating a number of transcription factors which affects the healthy lifespan. It activates catabolic pathways such as glucose uptake, glycolysis, fatty acid uptake, and fatty acid oxidation. AMPK also induces mitochondrial biogenesis, most likely by directly phosphorylating PGC1α.

Mitophagy

2012-05-20T14:46:48Z

New page

{{MitoPedia
|abbr=Mitophagy
|info=Green, D. R.; Galluzzi, L. & Kroemer, G. Mitochondria and the autophagy-inflammation-cell death axis in organismal aging. Science, 2011, 333, 1109-1112
}}
{{MitoPedia methods
|mitopedia method=Respirometry, Fluorometry
}}
{{MitoPedia topics}}
Autophagy (self-eating) in general is viewed as a degradation process which removes non-essential or damaged cellular constituents. '''Mitophagy''', which is specifically targeted to mitochondria, eliminates dysfunctional or damaged mitochondria. During the course of life, mitochondrial genomes accumulate mutations that impair respiration and can lead to excessive [[ROS]]. ROS is also a well-known side product of normal [[respiration]] and can damage other organelles. By eliminating damaged or dysfunctional components of the cell and the mitochondrion, mitophagy is an important mechanism in the cellular adaptation to stress and serves as a quality-control ensuring proper mitochondrial and cell function.

'''Mechanism'''

Autophagy, or in mitochondrial terms, mitophagy occurs by the formation of autophagosomes. These essentially double-membraned vesicles sequester damaged organelles, proteins, or portions of the cytoplasm, which then fuse with lysosomes. After being fused, the sequestered contents are degraded by the acidic environment of lysosomal enzymes. In order to accomplish this task, more than 30 Atg (AuTophaGy-related) proteins are recruited.

Talk:Open access

2012-05-20T13:59:31Z

New page

== Thoughts on publication strategies ==
* Can an open access journal use the wiki platform, with login limited to editors (and reviewers), to keep costs low and provide effective search options?
* How can the substantial labour be financed, if neither author fees (page charges) nor user fees (open access) add to be budget? - If nothing is charged, how can it be sold?
::* A minimum submission fee may be charged, which may be waved in specific cases to maintain a fair access to submission of a publication.
::* Suppport by conferences publishing their abstracts or proceedings in the open access journal.
::* Page charges may be voluntary, and articles can be labelled as (a) voluntary page charges based on the availability of financial support (grants, institutional support, etc.) - all authors should be explicitely contacted asking for such support, particularly if grants are cited, (b) voluntary page charges considered as a donation, (c) minor contributions. The financial aspects must not be disclosed during the review process, to guarantee an unbiased review with respect to any payments.
::* Company-supported articles with obligatory page charges.
::* Support by a scientific society (MiPs ?). E.g. members of a society (MiPs) may receive login information and thus may increase the critical mass of scientists who contribute directly to discussions, compared to the indirect contributions via Email to the editors.
::* Paid advertisements (companies) and announcements (conferences etc).
::* General institutional financial support (?).

=== Evolution of an open access publication ===
:: Some of these thoughts may not be practical and provide merely a basis for further brainstorming.
# The manuscript (MS) is put on-line as submitted (pdf for permanent track-record). The on-line access may be (a) open for all, or (b) open for the editors only (??).
# An alert is circulated to all editors and to selected reviewers, who should add their comments non-anonymously to the website, within a defined time frame (e.g. 1 month or 3 weeks). The editors and invited reviewers may modify their evaluation during the editorial period, and discuss evaluations of other editors/reviewers. Since all information is open-source, any conflict of interests are transparent (e.g. if an editor is an author). The authors get an immediate feedback from the on-line comments if access is 'open for all'.
# A specific editor (without conflict of interest) is nominated to summarize all comments, taking into account conflicts of interests (if editors are authors), and reach a first-level decision: Is the MS to be considered for (a) final publication, (b) revision, (c) rejection (pdf for permanent track-record). Authors may respond to rejections, and a different editor will reach a final evaluation.
# Upon request of the authors, a finally rejected MS is deleted. Alternatively, it may remain on-line as an 'unpublished MS', together with the editors comments and the rebuttal of the authors. This provides the chance of formally resubmitting an initially rejected MS with appropriate arguments.
# Final publications (PUB) are moved from the MS to the PUB category. (The MS category may be on a different website, or in a different category of the same website.)
# A PUB is subject to further evolution. (a) Supplementary materials may be added after publication (letter to the Editor, simple decision by the editor). (b) A PUB may evolve into a new version, which may be more useful and efficient than a ‘new’ publication (editorial process?). (c) Readers like authors may submit their comments to the editor, who decides on adding these comments to the website.
::* Even when trying the best in completion of a publication, there is generally scope for making it better.
::* Fair citation is implemented by the possibility to add references newly discovered by the authors, or upon request by readers and communicated to the editor. As a reader-friendly approach, (a) main citations may be limited to a defined number (depending on article tye), and (b) an unlimited number of references may be added under 'additional references' - and this is open for comments.

=== Author information ===
* Provide information on the specific responsibilities of each co-author (this is standard in many journals).
* Follow transparent rules particulary for the two major positions of the first and senior authors.
* Define 'conflict of interest': For most (not all) scientists, a publication is written with the clear financial interests. These interests may be related to obtain a degree (was this publication part of a PhD or other thesis?), another grant, a new or better position. Is this then more or less biased compared to the conventional conflict of interest statements? This is so trivial and clear, that a general statement may not be necessary, such as "''This publication supports financial and career interests of authors A, B, C, ...)''".

Open access

2012-05-20T11:39:19Z

Created page with "== Open access and Gentle Science == Published scientific information – largely supported by the society - should be accessible in general, without separation of privileged ..."

New page

== Open access and Gentle Science ==

Published scientific information – largely supported by the society - should be accessible in general, without separation of privileged ‘rich’ institutions and limited access in underdeveloped countries. Open access and open-source initiatives should be supported in the spirit of [[Gentle Science]].

=== Primary aims ===
# Summarize relevant information on the present state of discussion on 'open access publishing',
# Collect some critical reviews on these sources of information,
# Extend the discussion in the spirit of Gentle Science,
# Generate a comprehensive list on open access publication in mitochondrial physiology, if a conclusion is reached.

=== Some well-known facts ===
:* Particularly young scientists may be forced to prioritize high-impact publication for securing progress in their career, which then places considerations on open access at a low rank.
:* Some open access journals have higher publication fees compared to non-open access journals, to be covered by the authors. This leads to different ratings of 'open'.
:* Some scientists complete and publish their theses (PhD and other), without ever facing in their education any discussion on 'open access publication'.

== Some links to Open access ==
:* http://en.wikipedia.org/wiki/Open_access; compare: http://en.wikipedia.org/wiki/Open_science
:* http://www.earlham.edu/~peters/fos/overview.htm
:* http://www.arl.org/sparc/openaccess/
:* http://www.earlham.edu/~peters/fos/bethesda.htm
:* http://www.doaj.org/doaj?func=loadTempl&templ=links&uiLanguage=en
:* http://scholarlyoa.com/
:* http://www.freejournalsact.com

* To add information (continue the discussion, suggest links etc.) you may log in or send us information by Email; in any case, please contact [[Harrison DK|Dr. David Harrison]] (Email: d.k.harrison@ncl.ac.uk ).

{{Gentle Science}}

Gentle Science

2012-05-20T11:29:57Z

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	__FORCETOC__		__FORCETOC__

-	'''Gentle Science''' recognizes the special responsibility of the scientific community, for the quality of science, the quality of life in science, and its mission. While the individual scientist contributes her/his share, the scientific community requires concerted actions to encourage Gentle Science on institutional, national and world-wide levels.	+	'''Gentle Science''' recognizes the special responsibility of the scientific community, for the quality of science, the quality of life in science, and its mission. While the individual scientist contributes her/his share, the scientific community requires concerted actions to encourage Gentle Science on institutional, national and world-wide levels [[#Notes\|[1,2]]].
-		+

		+
	== Quotes ==		== Quotes ==
	*For first steps, see: [http://www.oroboros.at/index.php?gentle-science 'powerful, efficient, and more gentle ..'].		*For first steps, see: [http://www.oroboros.at/index.php?gentle-science 'powerful, efficient, and more gentle ..'].
-	*~~Gentle Science recognizes the special responsibility of the scientific community, for the quality of~~ science, the quality of life in science, and its mission. While the individual scientist contributes her/his share, the scientific community requires concerted actions to encourage Gentle Science on institutional, national and world-~~wide levels~~ [[~~#Notes\|[1,2~~]]]	+	*Open science - [[open access]] - open source [[#Notes\|[3,4]]].
-	*Open science - open source [[#Notes\|[3,4]]]	+
-		+
	*Unexamined science is not worth practicing/publishing.		*Unexamined science is not worth practicing/publishing.
	*Gentle Science develops and implements the concept of Scientific Social Responsibility (SSR), complementary to Corporate Social Responsibility (CSR). Combine large scientific footprints with small environmental footprints; implement strategies of sustainability: climate change in the laboratory [[#Notes\|[5]]]		*Gentle Science develops and implements the concept of Scientific Social Responsibility (SSR), complementary to Corporate Social Responsibility (CSR). Combine large scientific footprints with small environmental footprints; implement strategies of sustainability: climate change in the laboratory [[#Notes\|[5]]]
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	== Notes ==		== Notes ==

-	#Does Gentle Science require a form of organization? – non-profit organization? – Gentle Science homepage? – Gentle Science network, linked on homepages – Gentle Science statements on homepages, Email signatures, letterheads – Encourage scientific societies and journals to engage in Gentle Science.	+	# Does Gentle Science require a form of organization? – non-profit organization? – Gentle Science homepage? – Gentle Science network, linked on homepages – Gentle Science statements on homepages, Email signatures, letterheads – Encourage scientific societies and journals to engage in Gentle Science.
-	#How can the scientific community provide positive feedback to the practice of Gentle Science, rather than supporting junk science (unfair citation hiding the priority of other groups; incomplete methods description, not disclosing important detail to potential competitors; presentation merely of published information at conferences, preventing open exchange on cutting-edge scientific progress; quick-and-dirty publication instead of implementation of QA, compromising quality for the sake of apparent priority; …)?	+	# How can the scientific community provide positive feedback to the practice of Gentle Science, rather than supporting junk science (unfair citation hiding the priority of other groups; incomplete methods description, not disclosing important detail to potential competitors; presentation merely of published information at conferences, preventing open exchange on cutting-edge scientific progress; quick-and-dirty publication instead of implementation of QA, compromising quality for the sake of apparent priority; …)?
-	#Published scientific information – largely supported by the society - should be accessible in general, without separation of privileged ‘rich’ institutions and limited access in underdeveloped countries. Open- access and open-source initiatives should be supported.	+	# Published scientific information – largely supported by the society - should be accessible in general, without separation of privileged ‘rich’ institutions and limited access in underdeveloped countries. [[Open access]] and open-source initiatives should be supported.
-	#Provide information on the specific responsibilities of each co-author in all publications: While an increasing number of journals requests author information, inclusion of this information should constitute a decision and responsibility of the authors even in cases when this information is not requested (for comparison, less important statements are found frequently in the acknowledgements section).	+	# Provide information on the specific responsibilities of each co-author in all publications: While an increasing number of journals requests author information, inclusion of this information should constitute a decision and responsibility of the authors even in cases when this information is not requested (for comparison, less important statements are found frequently in the acknowledgements section).
-	#Climate change in the laboratory: Unnecessary waste production can be limited in scientific institutions, by implementation of energy-efficient and material-efficient technologies. Dischargeable tools should be replaced by application of re-usable tools whenever possible. Scientific institutions should be rated on the basis of their positive scientific impact and their positive environmental impact factor.	+	# Climate change in the laboratory: Unnecessary waste production can be limited in scientific institutions, by implementation of energy-efficient and material-efficient technologies. Dischargeable tools should be replaced by application of re-usable tools whenever possible. Scientific institutions should be rated on the basis of their positive scientific impact and their positive environmental impact factor.
-	#Optimization instead of maximization is required in strategies of scientific publication. While scientific output is still rated frequently on a totally non-scientific basis of ‘number’ of publications, simple mechanisms may be implemented by the scientific community to encourage quality rather than quantity. In job applications and project applications, for instance, a personal selection of very few ‘high quality and relevant’ publications should be requested, without further consideration of numbers of scientific publications (what are large numbers good for?).	+	# Optimization instead of maximization is required in strategies of scientific publication. While scientific output is still rated frequently on a totally non-scientific basis of ‘number’ of publications, simple mechanisms may be implemented by the scientific community to encourage quality rather than quantity. In job applications and project applications, for instance, a personal selection of very few ‘high quality and relevant’ publications should be requested, without further consideration of numbers of scientific publications (what are large numbers good for?).
-	#Evolution of a scientific publication: Even when trying the best in completion of a publication, there is generally scope for making it better. Whereas a printed ‘paper’ is a final document of an original publication, any published pdf file can potentially be edited for further improving the quality of a publication (corrections, additions, re-interpretations, even short discussions). For instance, fair citation may not always be possible in the most optimal way, given the constraints on page limits, maximum number of references, and the impossibility of complete awareness by the authors of further relevant references. Additions, corrections and extensions are possible, however, in the form of supplementary materials that may be added even after publication, particularly on the basis of correspondence that may be initiated only after publication. As long as journals do not include supplementary materials after publication, this may be achieved by institutional or other homepages etc., where sections are linked to the relevant publications. Corrections and additions may then not be limited to ‘fair citations', but be extended to all other relevant supplementary information, which may be more useful and efficient than a ‘new’ publication.	+	# Evolution of a scientific publication: Even when trying the best in completion of a publication, there is generally scope for making it better. Whereas a printed ‘paper’ is a final document of an original publication, any published pdf file can potentially be edited for further improving the quality of a publication (corrections, additions, re-interpretations, even short discussions). For instance, fair citation may not always be possible in the most optimal way, given the constraints on page limits, maximum number of references, and the impossibility of complete awareness by the authors of further relevant references. Additions, corrections and extensions are possible, however, in the form of supplementary materials that may be added even after publication, particularly on the basis of correspondence that may be initiated only after publication. As long as journals do not include supplementary materials after publication, this may be achieved by institutional or other homepages etc., where sections are linked to the relevant publications. Corrections and additions may then not be limited to ‘fair citations', but be extended to all other relevant supplementary information, which may be more useful and efficient than a ‘new’ publication.


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	At the dinner following the summary session of the QA Workshop on ‘Respirometry of Permeabilized Muscle Fibres: Towards Quality Assurance in the Diagnosis of Mitochondrial Function’ (2009 December 9-12; Innsbruck, Austria), the discussion turned to the limited degree of freedom available in our world of competitive science to implement quality rather than quantity in the publication strategies of scientists. We are all fighting with the overload of new publications, many of which lack the quality that would be desirable in the spirit of true progress. What would be an alternative? Are we catering for Fast Food (i.e. frequently junc food) in science? Do we need a Slow Food (Slow Science) movement? Then Shilpa Iyer proposed ‘Gentle Science’, and the response was clear and explicit: [http://www.oroboros.at/?Gentle-Science Gentle Science Shapes the World], signed by all participants at the dinner discussion (see Signatures; the table napkin was donated by the restaurant ‘Glasmalerei’; several workshop participants had to leave the QA workshop before the summary discussion)..		At the dinner following the summary session of the QA Workshop on ‘Respirometry of Permeabilized Muscle Fibres: Towards Quality Assurance in the Diagnosis of Mitochondrial Function’ (2009 December 9-12; Innsbruck, Austria), the discussion turned to the limited degree of freedom available in our world of competitive science to implement quality rather than quantity in the publication strategies of scientists. We are all fighting with the overload of new publications, many of which lack the quality that would be desirable in the spirit of true progress. What would be an alternative? Are we catering for Fast Food (i.e. frequently junc food) in science? Do we need a Slow Food (Slow Science) movement? Then Shilpa Iyer proposed ‘Gentle Science’, and the response was clear and explicit: [http://www.oroboros.at/?Gentle-Science Gentle Science Shapes the World], signed by all participants at the dinner discussion (see Signatures; the table napkin was donated by the restaurant ‘Glasmalerei’; several workshop participants had to leave the QA workshop before the summary discussion)..

-		+
	== Discussion ==		== Discussion ==

-	* Continue the discussion: [[Talk:Gentle Science]]	+	=== General discussion on Gentle Science ===
		+	* Continue the discussion: '''[[Talk:Gentle Science]]'''

		+	=== Open access publication ===
		+	: The topic of '''Open access publication''' should be taken into serious consideration by '''Gentle Science'''.
		+	* Continue the discussion: '''[[Open access]]'''

	== Historical notes ==		== Historical notes ==

Bioblast manual: Formatting

2012-05-20T09:27:15Z

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	:# Until 2011-Oct: A short 'slang' acronym, such as JEB, to keep the article name short. No standardization is possible, since not all journals have commonly used 'slang' acronyms, and the acronym is different from the standardized abbreviation used in the full reference.		:# Until 2011-Oct: A short 'slang' acronym, such as JEB, to keep the article name short. No standardization is possible, since not all journals have commonly used 'slang' acronyms, and the acronym is different from the standardized abbreviation used in the full reference.
	:# Until 2011-Nov-21: Standardized abbreviation, with punctuation, as used in the full reference until Nov 2011, such as J. Exp. Biol. The final dot in the article name, however, is truncated when the weblink is copied, such that the copied weblink becomes dysfunctional.		:# Until 2011-Nov-21: Standardized abbreviation, with punctuation, as used in the full reference until Nov 2011, such as J. Exp. Biol. The final dot in the article name, however, is truncated when the weblink is copied, such that the copied weblink becomes dysfunctional.
		+
		+	== Format of figures ==
		+	* Several figures do not change size when the zoom of the screen is modified, hence they change in proportion with the text. In many cases, a zoom of 125% is considered as a standard [Ctrl-O]. Therefore, formatting of such figures should be optimized at a zoom of 125%.
		+	::* Example: 933px in OROBOROPEDIA [[Template:Mainpage welcomebox title]].

Template:Mainpage welcomebox title

2012-05-20T09:13:45Z

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-	[[File:Nordkette-Innsbruck from OROBOROS Office 2012-12-23.jpg\|~~1100px~~\|center]]	+	[[File:Nordkette-Innsbruck from OROBOROS Office 2012-12-23.jpg\|933px\|center]]
	'''Bioblast''' - wiki by [http://www.oroboros.at OROBOROS INSTRUMENTS]		'''Bioblast''' - wiki by [http://www.oroboros.at OROBOROS INSTRUMENTS]

AMPK

2012-05-20T02:47:49Z

New page

{{MitoPedia
|abbr=AMPK
|description=AMP-activated protein kinase
|info=Hardie, D. G.; Ross, F. A. & Hawley, S. A. AMPK: a nutrient and energy sensor that maintains energy homeostasis. Nat Rev Mol Cell Biol, 2012, 13, 251-262

Steinberg, G. R. & Kemp, B. E. AMPK in Health and Disease. Physiol Rev, 2009, 89, 1025-1078
}}
{{MitoPedia methods}}
{{MitoPedia topics
|mitopedia topic=Enzyme, Substrate and metabolite
}}
'''AMPK''' is a regulatory protein which acts as crucial cellular energy sensor by sensing AMP, ADP and/or Ca2+ levels in response to metabolic stresses or drug administration. AMPK can also be activated by reactive oxygen species (ROS) such as hydrogen peroxide (H2O2). Basically, it regulates energy balance by activating catabolic pathways that generate ATP while conserving ATP by downregulating anabolic pathways. AMPK is a heterotrimeric protein (catalytic α-subunit and regulatory β- and γ-subunits). The well-known oral antidiabetic drug metformin, thiazolidinediones, resveratrol and AICAR as well as many other xenobiothics exerts their mechanism of action by activating AMPK.

'''Activation'''

Severe cellular energy stress causes a rise in AMP/ATP and ADP/ATP ratios. Upon binding of AMP and - as has recently been found - ADP to regulatory γ-subunit Thr172 is phosphorylated by upstream kinase LKB1–STRAD–MO25 complex or, alternatively, by Ca2+/calmodulin-activated protein kinase kinase, CaMKKβ. CaMKKβ, however, senses Ca2+ levels rather than changes in adenine nucleotides. Upon activation, AMPK upregulates genes involved in oxidative metabolism and oxidative stress resistance by regulating a number of transcription factors which affects the healthy lifespan. It activates catabolic pathways such as glucose uptake, glycolysis, fatty acid uptake, and fatty acid oxidation. AMPK also induces mitochondrial biogenesis, most likely by directly phosphorylating PGC1α.

Gentle Science

2012-05-19T15:43:45Z

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	== QA and Gentle Science ==		== QA and Gentle Science ==

-	At the dinner following the summary session of the QA Workshop on ‘Respirometry of Permeabilized Muscle Fibres: Towards Quality Assurance in the Diagnosis of Mitochondrial Function’ (2009 December 9-12; Innsbruck, Austria), the discussion turned to the limited degree of freedom available in our world of competitive science to implement quality rather than quantity in the publication strategies of scientists. We are all fighting with the overload of new publications, many of which lack the quality that would be desirable in the spirit of true progress. What would be an alternative? Are we catering for Fast Food (i.e. frequently junc food) in science? Do we need a Slow Food (Slow Science) movement? Then Shilpa Iyer proposed ‘Gentle Science’, and the response was clear and explicit: [http://www.oroboros.at/~~index.php~~?~~gentle~~-~~science~~ Gentle Science Shapes the World], signed by all participants at the dinner discussion (see Signatures; the table napkin was donated by the restaurant ‘Glasmalerei’; several workshop participants had to leave the QA workshop before the summary discussion)..	+	At the dinner following the summary session of the QA Workshop on ‘Respirometry of Permeabilized Muscle Fibres: Towards Quality Assurance in the Diagnosis of Mitochondrial Function’ (2009 December 9-12; Innsbruck, Austria), the discussion turned to the limited degree of freedom available in our world of competitive science to implement quality rather than quantity in the publication strategies of scientists. We are all fighting with the overload of new publications, many of which lack the quality that would be desirable in the spirit of true progress. What would be an alternative? Are we catering for Fast Food (i.e. frequently junc food) in science? Do we need a Slow Food (Slow Science) movement? Then Shilpa Iyer proposed ‘Gentle Science’, and the response was clear and explicit: [http://www.oroboros.at/?Gentle-Science Gentle Science Shapes the World], signed by all participants at the dinner discussion (see Signatures; the table napkin was donated by the restaurant ‘Glasmalerei’; several workshop participants had to leave the QA workshop before the summary discussion)..


-	== ~~Historical notes~~ ==	+	== Discussion ==

-		+	* Continue the discussion: [[Talk:Gentle Science]]
		+
		+
		+	== Historical notes ==
	* Made history - publications on mitochondria collected in the spirit of Gentle Science: [[Mitochondria and bioblasts: History]]		* Made history - publications on mitochondria collected in the spirit of Gentle Science: [[Mitochondria and bioblasts: History]]
	* Fritz Pregl: "Pregl had, in the early stages of his investigations, avoided publishing individual reports on his experiments, until he had convinced himself that his methods did not only work in his own, but also in other laboratories. .. Following the award of the Nobel Prize for Chemistry in 1923, chemists from all over the world came to the Medico-Chemical Institute in Graz to study Pregl's techniques of quantitative organic micro-analysis under his guidance." [http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1923/pregl-bio.html The Nobel Prize in Chemistry 1923]		* Fritz Pregl: "Pregl had, in the early stages of his investigations, avoided publishing individual reports on his experiments, until he had convinced himself that his methods did not only work in his own, but also in other laboratories. .. Following the award of the Nobel Prize for Chemistry in 1923, chemists from all over the world came to the Medico-Chemical Institute in Graz to study Pregl's techniques of quantitative organic micro-analysis under his guidance." [http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1923/pregl-bio.html The Nobel Prize in Chemistry 1923]

-
-	~~== Discussion ==~~
-
-	* Continue the discussion: [[Talk:Gentle Science]]

	== Network ==		== Network ==

Talk:Gentle Science

2012-05-19T15:24:21Z

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	* [[Gentle Science]] has been accessed >5,000 times (2012-03-17).		* [[Gentle Science]] has been accessed >5,000 times (2012-03-17).

-	== ~~Erich Gnaiger, 31 December 2009~~ ==	+	== Comments on Gentle Science ==

-	~~Dear Gentle Scientists:~~	+	== [[Harper ME\|Mary-Ellen Harper]] 2012-03-25 ==

-	~~It was a memorable dinner at~~ the ~~conclusion~~ of ~~our QA workshop in the restaurant 'Glasmalerei' (window painting), a gentle discussion on~~ Gentle Science~~. Gentle Science is far from an illusion or idealistic picture of humanistic science~~, far from a soft 'alternative' dream of a better non-achievable world. I compare Gentle Science to sports: At its best, good sports is fair, tough and playful, sometimes extreme and sometimes balanced, not a necessity but an added value, exciting within the ~~full range of fun and pain, within the freedom provided by well defined rules, and always attacked by the crippling methods of braking the rules. The real losers~~ are ~~those who believe~~ in those who break the rules, it is less clear who are the winners: the players, the teams, the 'subjects' (medicine, environment, students, technologies), or backstage figures who are not even part of the 'game', ..?	+	Personally, I certainly appreciate the importance of Gentle Science, especially in the very competitive funding climate that we all are trying to work in!

		+	== [[Shick JM\|J Malcolm Shick]] 2011-09-26 ==

-	~~To me, there is no alternative to Gentle Science, otherwise I would have to change my profession~~ as ~~a scientist, and I would have~~ to ~~abandon my perspective of instrumental development and quit OROBOROS INSTRUMENTS and high-resolution respirometry. Gentle Science is~~ a ~~reality -~~ the ~~high interest in our QA workshop provided a very nice example. Hence it~~ is ~~worthwhile to give it a voice,~~ and ~~to make it happen on~~ an explicit ~~and conscientious basis~~. ~~Further discussions during the O2k-Workshop on HRR resulted in very positive feedback~~.	+	You mention "slow food" as contributing terminology to various "slow" movements (a traffic slogan in the US is "slow down and live"). I found an explicit mention of this elsewhere (''Nature'', no less): http://www.nature.com/nature/journal/v443/n7109/full/443271e.html

		+	== [[Garcia-Roves PM\|Pablo M Garcia-Roves]] 2010-01-14 ==

-	~~An attempt~~ of ~~collecting some summary notes (during our trip from Schroecken back~~ to ~~Innsbruck) is~~ now ~~available as a first draft~~ on ~~our website under 'Links'~~.	+	Thanks for the summary of the Gentle Science movement. I have read the points and I like the first draft, I don't have any thing to add right now but I hope we keep working on that idea and I hope reality for some scientist.

		+	== [[Votion DM\|Dominique-Marie Votion]] 2010-01-12 ==

-	Perhaps .. you may find the time to take a look at the short summary; add your bits and pieces; make your corrections, deletions, and extensions; and provide suggestions for possible next steps. There is great potential in a 'Gentle Science~~' movement, with~~ a ~~very thin borderline between~~ (i) ~~a merely trivial collection of simply 'good' things~~, ~~or (ii) a convincing concept of what is directly needed now~~ and ~~in the future~~. ~~I am looking forward to adding your~~ Gentle Science ~~suggestions to further updates~~.	+	Gentle Science is a necessity for those who want to respect patients (horses in my case but also their owner), Science and ultimately, themselves. Gentle Science is a peaceful battle that we have committed every day.

		+	== [[Hansson M\|Magnus Hansson]] 2010-01-12 ==

-	~~With the very best wishes for the New Year 2010, in the spirit of Gentle Science,~~	+	A great and gentle summary! Magnus

-	~~[[Gnaiger E\|Erich]]~~	+	== [[Sumbalova Z\|Zuzana Sumbalova]] 2010-01-12 ==
-		+
-	== [[~~Kane DA~~\|~~Daniel Alan Kane~~]]~~, 02 January~~ 2010 ==	+
-	I have .. been thinking more and more about the approaches toward Gentle Science and how it can be effectively communicated. I feel that your summary is an excellent start. I would like to add something that is perhaps so fundamental to Gentle Science that it may be unnecessary to include:	+
-		+
-	Science has been defined as "The knowledge or a system of knowledge covering general truths or the operation of general laws especially as obtained and tested through scientific method" (http://www.merriam-webster.com/dictionary/science). Gentle Science balances the "systematic acquisition of knowledge based on the scientific method" (http://en.wikipedia.org/wiki/Science) with thorough reflection upon these systems and methods. This is akin to the statement by Socrates that "The unexamined life is not worth living..." (Plato, Apology, 38a; http://en.wikiquote.org/wiki/Socrates). An adaptation might be "unexamined science is not worth practicing/publishing." However, in a more practical sense, the examination of science may involve considering science while keeping in mind the items outlined in our website draft. This notion of reflection/examination/awareness may also then overlap with MiPArt and other artistic approaches.	+

		+	I really appreciated the atmosphere of the QA meeting with its open discussions and I think that this type of meetings should be absolutely essential in our work, because we all are colleagues working on the same thing. We all want to know exact mechanisms of diseases and have efficient tools for their therapy. I was very impressed by the ideas of gentle science. We all have to keep these ideas in our minds in our everyday work so they can come true. I am ready for that. With best wishes to gentle science, Zuzana

-	== [[Iyer S\|Shilpa Iyer]]~~, 01 January~~ 2010 ==	+	== [[Iyer S\|Shilpa Iyer]] 2010-01-01 ==

	The contents of .. the summary link for QA workshop touched my heart. As I was sitting and reading the information presented on our web page, my unruly fingers typed out the thoughts to you. As this verse goes....		The contents of .. the summary link for QA workshop touched my heart. As I was sitting and reading the information presented on our web page, my unruly fingers typed out the thoughts to you. As this verse goes....
Line 77:		Line 77:


-	Einstein said,~~” Most~~ of the fundamental ideas of science are essentially simple and may as a rule be expressed in a language comprehensible to everyone.” Yes, you are so right.. “GS” should not be treated as a trivial or light hearted concept. It is in fact a movement which aims towards contributing to the elevation of the human race and human life. Gentle science is a wake up call urging all of us to understand the intellectual work be it creative or receptive. It is a contemporary thought built upon an ancient concept. As an artist scientist all I can say is this movement is a hidden, intricate and beautiful fractal order underlying all seemingly chaotic fast paced scientific events. We as individuals can be personified as patterns relaying the simple unifying message in infinite variations and themes to revolutionize the view of the scientific world. Gentle Science basically aims to create a bridge between science and spirituality and applies this knowledge to better understand our own life and to live in harmony within our selves and with the universe around us. What we are really trying to achieve is a genesis of new ideas to reform our society.	+	Einstein said, ”Most of the fundamental ideas of science are essentially simple and may as a rule be expressed in a language comprehensible to everyone.” Yes, you are so right.. “GS” should not be treated as a trivial or light hearted concept. It is in fact a movement which aims towards contributing to the elevation of the human race and human life. Gentle science is a wake up call urging all of us to understand the intellectual work be it creative or receptive. It is a contemporary thought built upon an ancient concept. As an artist scientist all I can say is this movement is a hidden, intricate and beautiful fractal order underlying all seemingly chaotic fast paced scientific events. We as individuals can be personified as patterns relaying the simple unifying message in infinite variations and themes to revolutionize the view of the scientific world. Gentle Science basically aims to create a bridge between science and spirituality and applies this knowledge to better understand our own life and to live in harmony within our selves and with the universe around us. What we are really trying to achieve is a genesis of new ideas to reform our society.
		+
		+	== [[Kane DA\|Daniel Alan Kane]], 2010-01-02 ==
		+	I have .. been thinking more and more about the approaches toward Gentle Science and how it can be effectively communicated. I feel that your summary is an excellent start. I would like to add something that is perhaps so fundamental to Gentle Science that it may be unnecessary to include:

-	~~===New address===~~	+	Science has been defined as "The knowledge or a system of knowledge covering general truths or the operation of general laws especially as obtained and tested through scientific method" (http://www.merriam-webster.com/dictionary/science). Gentle Science balances the "systematic acquisition of knowledge based on the scientific method" (http://en.wikipedia.org/wiki/Science) with thorough reflection upon these systems and methods. This is akin to the statement by Socrates that "The unexamined life is not worth living..." (Plato, Apology, 38a; http://en.wikiquote.org/wiki/Socrates). An adaptation might be "unexamined science is not worth practicing/publishing." However, in a more practical sense, the examination of science may involve considering science while keeping in mind the items outlined in our website draft. This notion of reflection/examination/awareness may also then overlap with MiPArt and other artistic approaches.

-	~~Shilpa Iyer, PhD~~	+	== [[Gnaiger E\|Erich Gnaiger]] 2009-12-31 ==
-	~~Research Assistant Professor~~	+	Dear Gentle Scientists:
-	~~Center for the Study of Biological Complexity~~	+
-	~~Life Sciences Program~~	+
-	~~Virginia Commonwealth University~~	+
-	~~Richmond, VA 23284~~	+
-	~~siyer@vcu.edu~~	+

-	~~== [[Votion DM\|Dominique~~-~~Marie Votion]]~~, ~~12 January 2010 ==~~	+	It was a memorable dinner at the conclusion of our QA workshop in the restaurant 'Glasmalerei' (window painting), a gentle discussion on Gentle Science. Gentle Science is far from an illusion or idealistic picture of humanistic science, far from a soft 'alternative' dream of a better non-achievable world. I compare Gentle Science to sports: At its best, good sports is fair, tough and playful, sometimes extreme and sometimes balanced, not a necessity but an added value, exciting within the full range of fun and pain, within the freedom provided by well defined rules, and always attacked by the crippling methods of braking the rules. The real losers are those who believe in those who break the rules, it is less clear who are the winners: the players, the teams, the 'subjects' (medicine, environment, students, technologies), or backstage figures who are not even part of the 'game', ..?

-	Gentle Science is a necessity for those who want to respect patients (horses in my case but also their owner), Science and ultimately, themselves. Gentle Science is a peaceful battle that we have committed every day.

-	~~== [[Hansson M\|Magnus Hansson]]~~, ~~12 December 2010 ==~~	+	To me, there is no alternative to Gentle Science, otherwise I would have to change my profession as a scientist, and I would have to abandon my perspective of instrumental development and quit OROBOROS INSTRUMENTS and high-resolution respirometry. Gentle Science is a reality - the high interest in our QA workshop provided a very nice example. Hence it is worthwhile to give it a voice, and to make it happen on an explicit and conscientious basis. Further discussions during the O2k-Workshop on HRR resulted in very positive feedback.

-	~~A great and gentle summary! Magnus~~

-	~~== [[Subalova Z\|Zuzana Sumbalova]], 12 January 2010 ==~~	+	An attempt of collecting some summary notes (during our trip from Schroecken back to Innsbruck) is now available as a first draft on our website under 'Links'.

-	I really appreciated the atmosphere of the QA meeting with its open discussions and I think that this type of meetings should be absolutely essential in our work, because we all are colleagues working on the same thing. We all want to know exact mechanisms of diseases and have efficient tools for their therapy. I was very impressed by the ideas of gentle science. We all have to keep these ideas in our minds in our everyday work so they can come true. I am ready for that. With best wishes to gentle science,

-	~~== [[Garcia-Roves PM\|Pablo M Garcia-Roves]]~~, ~~14 January 2010 ==~~	+	Perhaps .. you may find the time to take a look at the short summary; add your bits and pieces; make your corrections, deletions, and extensions; and provide suggestions for possible next steps. There is great potential in a 'Gentle Science' movement, with a very thin borderline between (i) a merely trivial collection of simply 'good' things, or (ii) a convincing concept of what is directly needed now and in the future. I am looking forward to adding your Gentle Science suggestions to further updates.

-	Thanks for the summary of the Gentle Science movement. I have read the points and I like the first draft, I don't have any thing to add right now but I hope we keep working on that idea and I hope reality for some scientist.

-	~~== [[Shick JM\|J. Malcolm Shick]]~~, ~~26 September 2011 ==~~	+	With the very best wishes for the New Year 2010, in the spirit of Gentle Science,

-	You mention "slow food" as contributing terminology to various "slow" movements (a traffic slogan in the US is "slow down and live"). I found an explicit mention of this elsewhere (''Nature'', no less): http://www.nature.com/nature/journal/v443/n7109/full/443271e.html	+	[[Gnaiger E\|Erich]]

Gentle Science

2012-05-19T15:09:12Z

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(One intermediate revision not shown)
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	== Historical notes ==		== Historical notes ==

		+
		+	* Made history - publications on mitochondria collected in the spirit of Gentle Science: [[Mitochondria and bioblasts: History]]
	* Fritz Pregl: "Pregl had, in the early stages of his investigations, avoided publishing individual reports on his experiments, until he had convinced himself that his methods did not only work in his own, but also in other laboratories. .. Following the award of the Nobel Prize for Chemistry in 1923, chemists from all over the world came to the Medico-Chemical Institute in Graz to study Pregl's techniques of quantitative organic micro-analysis under his guidance." [http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1923/pregl-bio.html The Nobel Prize in Chemistry 1923]		* Fritz Pregl: "Pregl had, in the early stages of his investigations, avoided publishing individual reports on his experiments, until he had convinced himself that his methods did not only work in his own, but also in other laboratories. .. Following the award of the Nobel Prize for Chemistry in 1923, chemists from all over the world came to the Medico-Chemical Institute in Graz to study Pregl's techniques of quantitative organic micro-analysis under his guidance." [http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1923/pregl-bio.html The Nobel Prize in Chemistry 1923]

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	E-mail: zuzana.jilkova@email.cz		E-mail: zuzana.jilkova@email.cz

-		+
-	~~== Comments on Gentle Science ==~~	+
-		+
-	::* [[Harper ME\|Dr. Mary-Ellen Harper, University of Ottawa, Canada]]: ''Personally, I certainly appreciate the importance of Gentle Science, especially in the very competitive funding climate that we all are trying to work in!'' (2012-03-25)	+
-		+


	{{Gentle Science}}		{{Gentle Science}}

MediaWiki:Sidebar

2012-05-19T07:27:50Z

Gnaiger 2000 Transpl Int

2012-05-19T07:09:32Z

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	\|organism=Human		\|organism=Human
	\|tissues=Endothelial; Epithelial; Mesothelial Cell		\|tissues=Endothelial; Epithelial; Mesothelial Cell
-	\|preparations=Intact Cell; Cultured; Primary, Oxidase; Biochemical Oxidation	+	\|preparations=Intact Cell; Cultured; Primary, Permeabilized cells, Oxidase; Biochemical Oxidation
	\|topics=Respiration; OXPHOS; ETS Capacity, Coupling; Membrane Potential, Ion Homeostasis		\|topics=Respiration; OXPHOS; ETS Capacity, Coupling; Membrane Potential, Ion Homeostasis
	\|discipline=Mitochondrial Physiology, Biomedicine		\|discipline=Mitochondrial Physiology, Biomedicine
	}}		}}

Stadlmann 2002 Transplantation

2012-05-19T07:09:13Z

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	\|organism=Human		\|organism=Human
	\|tissues=Endothelial; Epithelial; Mesothelial Cell		\|tissues=Endothelial; Epithelial; Mesothelial Cell
-	\|preparations=Intact Cell; Cultured; Primary	+	\|preparations=Intact Cell; Cultured; Primary, Permeabilized cells
	\|topics=Respiration; OXPHOS; ETS Capacity, Coupling; Membrane Potential, Substrate; Glucose; TCA Cycle		\|topics=Respiration; OXPHOS; ETS Capacity, Coupling; Membrane Potential, Substrate; Glucose; TCA Cycle
	\|additional=Latent mitochondrial dysfunction, Environmental Physiology; Toxicology		\|additional=Latent mitochondrial dysfunction, Environmental Physiology; Toxicology
	\|discipline=Mitochondrial Physiology, Biomedicine		\|discipline=Mitochondrial Physiology, Biomedicine
	}}		}}

Renner 2003 Biochim Biophys Acta

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	\|organism=Human		\|organism=Human
	\|tissues=Blood Cell; Suspension Culture		\|tissues=Blood Cell; Suspension Culture
-	\|preparations=Intact Cell; Cultured; Primary, Oxidase; Biochemical Oxidation, Enzyme	+	\|preparations=Intact Cell; Cultured; Primary, Permeabilized cells, Oxidase; Biochemical Oxidation, Enzyme
	\|topics=Respiration; OXPHOS; ETS Capacity, Coupling; Membrane Potential, Mitochondrial Biogenesis; Mitochondrial Density		\|topics=Respiration; OXPHOS; ETS Capacity, Coupling; Membrane Potential, Mitochondrial Biogenesis; Mitochondrial Density
	\|additional=Pharmacology; Biotechnology		\|additional=Pharmacology; Biotechnology
	\|discipline=Mitochondrial Physiology, Biomedicine		\|discipline=Mitochondrial Physiology, Biomedicine
	}}		}}