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Why you (scientists) should
          start blogging

                        Enro
             http://www.cafe-sciences.org



       Swiss Center for Affective Sciences,
14/11/2008    Geneva, Switzerland             1
Curriculum
• Engineer in Agricultural Sciences
• MSc in Social Studies of Science
• Blogger since 2003 as “Enro”, science
  blogger since 2006
• Co-founder of the science blogs
  community “C@fé des sciences”
• President of the French association
  “C@fetiers des sciences”

                                          2
Find the blog post




                     3
This evening I am nose deep in the middle
                                                   It has been postulated that people in
of the new issue of The New England
                                                   Western societies are chronically
Journal of Medicine. The journal contains a
                                                   sleep deprived, since the average
very interesting synopsis on the
                                                   sleep duration decreased from 9.0 to
presidential candidates' views on
                                                   7.5 hours during the 20th century.
reproductive freedom. If you completely
                                                   Therefore, it is important to examine
ignore the rest of my post (but, you won't
                                                   whether we can achieve beneficial
because it's going to be totally hot), read
                                                   effects with prolonged sleep. The
the reproductive freedom article.
                                                   finding that the possibility of
But, what has Dr. Isis all a twitter is actually
                                                   additional sleep seems to be
a piece of correspondence from Swedish
                                                   protective on the first workday after
researchers Imre Janszky and Rickard Ljung
                                                   the autumn shift is intriguing.
entitled “Shifts to and from Daylight Saving
                                                   Monday is the day of the week
Time and Incidence of Myocardial
                                                   associated with the highest risk of
Infarction”. Janszky and Ljung present a
                                                   acute myocardial infarction, with the
very intriguing data set. It's just a shame
                                                   mental stress of starting a new
their interesting data are confounded by
                                                   workweek and the increase in activity
their crappy interpretation.
                                                   suggested as an explanation. Our
Clearly Dr. Isis (…) must have been too
                                                   results raise the possibility that there
busy pouring herself a cocktail or staring at
                                                   is another, sleep-related component
her hotness in the mirror to notice their
                                                   in the excess incidence of acute
data showing that sleep deprivation was
                                                   myocardial infarction on Monday.
highest in women and people under 65.
Seasonal variations influencing circadian
One interesting observation from the
                                          behavior can be simulated by applying
studies of entrainment by skeleton
                                          different experimental photoperiods. A
photoperiods is the bistability
                                          photoperiod is described by the ratio of
phenomenon. A full photoperiod will
                                          light to darkness during a 24-hour cycle.
entrain the biological clock no matter
                                          Under laboratory conditions, summertime
how short or long is the photoperiod,
                                          light conditions are typically represented
i.e., the duration of the light portion
                                          by cycles of 18 hours light and 6 hours
of the light-dark cycle. Thus LD 1:23,
                                          dark or of 14 hours light and 10 hours
LD 3:21, LD 6:18, LD 8:16, LD 10:14,
                                          dark (LD 18:6 and LD 14:10, respectively),
LD 12:12, LD 14:10, LD 16:8, LD 18:6,
                                          whereas winter light conditions are
LD 21:3 and LD 23:1 are all equally
                                          mimicked by an LD 6:18 cycle or an LD
likely to entrain a clock. On the other
                                          10:14 cycle. In photoperiod experiments
hand, with skeleton photocycles,
                                          the external time of the Zeitgeber rhythm
photoperiod matters. The biological
                                          is specified as ExT (External Time) with
clock quot;prefersquot; short photoperiods to
                                          ExT12 corresponding to the middle of the
long photoperiods. Thus, when
                                          light-phase. Most laboratories use a rapid
exposed to a skeleton photocycle that
                                          transition from light to dark and from
attempts to entrain to a cycle
                                          dark to light and apply the same
mimicking a long photoperiod, the
                                          wavelength range and light intensity
rhythm will, instead, reverse the
                                          during the whole light period. However,
quot;nightquot; and quot;dayquot; (often with an abrupt
                                          this does not truly reflect natural lighting
phase-jump).
                                          conditions.
From one to many




    A personal tribune




                         6
From one to many

A personal tribune




                     A personal tribune




A personal tribune




                                          8
From one to many

                                          Reader
A personal tribune
                                                   Reader




                     A personal tribune




A personal tribune

                                  Reader

                                                            10
From one to many

                                          Reader
A personal tribune
                                                   Reader




                     A personal tribune




A personal tribune

                                  Reader

                                                            12
From one to many

                                          Reader
A personal tribune
                                                            Reader




                     A personal tribune



                                                   Reader

A personal tribune

                                  Reader

                                                                     14
What does it mean for
      research?
           Certified
          knowledge,
         instruments


          Institutions,
             peers




                          17
The Plant Cell, Vol. 17, 2856–2858, November 2005, www.plantcell.org ª 2005 American Society of Plant Biologists



LETTER TO THE EDITOR



A Toxic Mutator and Selection Alternative to the Non-Mendelian
RNA Cache Hypothesis for hothead Reversion

Lolle and colleagues observed frequent          toxic and mutagenic. The HTH gene en-              resulting in the enrichment of hth/HTH
true reversion of hothead (hth) mutations       codes a product whose closest character-           zygotes because the reversion rate was
of Arabidopsis thaliana, whereby up to 10%      ized relative is an MBC oxidoreductase that        much higher for pollen than for eggs (Figure
of the progeny of self-pollinated homozy-       hydrolyzes the aromatic mandelonitrile in          1B). Our selection hypothesis appears in-
gous hth/hth mutants carried a grandpa-         stone fruits (Zheng and Poulton, 1995)             consistent with the reported 3:1 progeny
rental HTH allele (Lolle et al., 2005).         (Figure 1A). Arabidopsis has complex met-          ratio from selfed heterozygotes because
Instability was not limited to the HTH          abolic pathways for the production of              selection in favor of HTH pollen should de-
gene: hth mutants displayed conversion          glucosinolates (Wittstock and Halkier,             crease the fraction of hth/hth progeny, but
of genome-wide polymorphisms to the             2002; Brown et al., 2003), some of which           HTH could have a paternal effect where an
genotype of a recent ancestor. The possi-       are aromatic and resemble mandelonitrile           hth/HTH heterozygous anther provides its
bility that a mutator phenotype caused          (Figure 1), and aromatic glucosinolates and        hth pollen with sufficient HTH enzyme
indiscriminate changes, thereby increasing      their derivatives are mutagenic (Musk et al.,      to avoid a crisis. An hth/hth anther would
the reversion rate of hth, was discounted       1995; Kassie et al., 1999; Kassie and              provide no enzyme. Selection favoring re-
because reverted HTH alleles showed no          Knasmuller, 2000; Canistro et al., 2004).          vertant cells could also act in the shoot
additional nucleotide changes, whereas 50       The sticky surface properties of the HTH           apical meristem, in the flower meristem,
to 100 changes per sequenced allele would       phenotype, which suggest alterations of            and in the anther primordia. In meristem
be expected from the ;5% hth reversion          cuticle, cell wall, and perhaps membranes,         tissues, selection could be influenced by
rate. These genetic instabilities were inter-   might also be an effect of the toxic mutator.      the defective cellular surface properties of
preted as a memory of a past genotypic             If an alternative genetic reservoir exists      hth mutants that lead to postgenital organ
state. A cache of double-stranded RNA           and it restores mutations to the previous          fusion (Lolle et al., 1998). Selection could
from the previous genotype was proposed,        genotype, it should be revised gradually           also act on seed, decreasing germination
which, at times of stress corrects mutated      so that its memory should fade with cell           of hth/hth zygotes in favor of HTH/hth
sites in a template-directed manner. The        divisions. Yet, data that addresses the            individuals.
existence of an alternate reserve genome        reversion rate are available in a previous            The precise reversion of hth mutations
appears consistent with the data and would      article by the same group and are inconsis-        without the appearance of secondary mu-
necessitate a revision of our theories of       tent with the above expectation (Lolle et al.,     tations is consistent with a template-driven
heredity. Two recent commentaries on this       1998). In complementation tests between            repair but also with the alternative hypoth-
discovery suggested that, instead of an         hth alleles, wild-type plants were observed        esis of mutagenesis and selection. As ex-
RNA cache, the hth-correcting mechanism         among the progeny of trans-heterozygotes           plained above, any significant mutation
depends on ectopic gene conversion              and were thought to result from intragenic         rate coupled to selection can yield frequent
(Chaudhury, 2005) or on an elusive DNA          recombination. These were almost certainly         revertants, and the probability of finding
cache (Ray, 2005). Thus, all explanations       revertants and not recombinants. The hth-          secondary mutations at HTH revertant
offered until now invoke novel genetic          10/hth-8 trans-heterozygote produced 30            alleles is proportional to the mutation rate.
phenomena. We offer an alternative expla-       wild types among 1858 individuals, whereas         In fact, the highest mutation rate compat-
nation based on established genetic and         hth-10/hth-4 produced only mutant prog-            ible with survival is likely to be significantly
evolutionary principles. HTH could be a meta-   eny (n ¼ 1629) (Lolle et al., 1998; Krolikowski    lower than the rates that would generate
bolic enzyme whose impairment causes            et al., 2003). The same alleles, hth-10 and        frequent concurrent mutations on the HTH
the accumulation of toxic and mutagenic         hth-4, were reported to revert in the 2005         gene. We know from TILLING experiments
compounds that act at random DNA sites.         article and to do so through multiple gen-         the genomic consequences of moderately
The observed high reversion rate of hth         erations (Lolle et al., 2005). Thus, the rate of   intense mutagenesis: in Arabidopsis, it pro-
What does it mean for
      research?
           Certified
          knowledge,
         instruments


          Institutions,
             peers
                                    Training,
                                  incorporated
                      Education       skills
                       system




                                                 30
What does it mean for
      research?
           Certified
          knowledge,
         instruments


          Institutions,
             peers
                                        Training,
                                      incorporated
                      Education           skills
                       system


                 Economic
                  system



                                  Competitive
                                  advantage,
                                   innovation        33
What does it mean for
      research?
                    Certified
                   knowledge,
                  instruments


                   Institutions,
                      peers
                                                 Training,
                                               incorporated
                               Education           skills
                                system


               Public      Economic
             authorities    system


    Collective goods,
                                           Competitive
    power, prestige,
                                           advantage,
         health,
                                            innovation        37
     environment...
What does it mean for
        research?
                            Certified
                           knowledge,
                          instruments


                           Institutions,
                              peers
                                                         Training,
  Expertise,
                                                       incorporated
popularization   Media, museums,       Education           skills
                  public forums         system


                       Public      Economic
                     authorities    system


            Collective goods,
                                                   Competitive
            power, prestige,
                                                   advantage,
                 health,
                                                    innovation        41
             environment...
Percentage of science news in Belgian newspapers
20



15



10



 5



 0
     Vif/L’Express   J. du Mardi    Le Soir   Libre Belgique Tendance       L’Echo   Dernière heure



                        http://www.belspo.be/belspo/home/publ/pub_ostc/Journ/rappULg_fr.pdf
Content of these science news



                                                        Technology




Medicine




                                                      Science




           http://www.belspo.be/belspo/home/publ/pub_ostc/Journ/rappULg_fr.pdf
Do you prefer that science information is presented to you…




                                                                 Other




Scientists




                                                         Journalists




                                   Special Eurobarometer 282, December 2007, p. 40
What could keep you from
        blogging
• Internally
 – time
 – hot science




                           48
What could keep you from
        blogging
• Internally
 – time
 – hot science
 – debating




                           50
What could keep you from
        blogging
• Internally
 – time
 – hot science
 – debating


• Externally
 – being scooped



                           52
What could keep you from
        blogging
• Internally
 – time
 – hot science
 – debating


• Externally
 – being scooped
 – lack of recognition
 – lack of visibility
                           54
©© alanak
©© Aurélien
Tabard
©© Manic Street
Preacher
The landscape of science
          blogs
• Communities, agregators




                            58
The landscape of science
          blogs
• Communities, agregators
• Rankings




                            64
The landscape of science
          blogs
• Communities, agregators
• Rankings
• Diversity
 –   scientists
 –   medicine doctors
 –   journalists
 –   engineers
 –   students
 –   teachers
 –   amateurs               67
Nine commandments
     before you start
• take your time
• be yourself
• match the form and the content
• write for everyone
• be transparent
• offer some eye candy
• be creative
• foster comments
• have fun!                        68

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Scientists should blog to share research widely

  • 1. Why you (scientists) should start blogging Enro http://www.cafe-sciences.org Swiss Center for Affective Sciences, 14/11/2008 Geneva, Switzerland 1
  • 2. Curriculum • Engineer in Agricultural Sciences • MSc in Social Studies of Science • Blogger since 2003 as “Enro”, science blogger since 2006 • Co-founder of the science blogs community “C@fé des sciences” • President of the French association “C@fetiers des sciences” 2
  • 3. Find the blog post 3
  • 4. This evening I am nose deep in the middle It has been postulated that people in of the new issue of The New England Western societies are chronically Journal of Medicine. The journal contains a sleep deprived, since the average very interesting synopsis on the sleep duration decreased from 9.0 to presidential candidates' views on 7.5 hours during the 20th century. reproductive freedom. If you completely Therefore, it is important to examine ignore the rest of my post (but, you won't whether we can achieve beneficial because it's going to be totally hot), read effects with prolonged sleep. The the reproductive freedom article. finding that the possibility of But, what has Dr. Isis all a twitter is actually additional sleep seems to be a piece of correspondence from Swedish protective on the first workday after researchers Imre Janszky and Rickard Ljung the autumn shift is intriguing. entitled “Shifts to and from Daylight Saving Monday is the day of the week Time and Incidence of Myocardial associated with the highest risk of Infarction”. Janszky and Ljung present a acute myocardial infarction, with the very intriguing data set. It's just a shame mental stress of starting a new their interesting data are confounded by workweek and the increase in activity their crappy interpretation. suggested as an explanation. Our Clearly Dr. Isis (…) must have been too results raise the possibility that there busy pouring herself a cocktail or staring at is another, sleep-related component her hotness in the mirror to notice their in the excess incidence of acute data showing that sleep deprivation was myocardial infarction on Monday. highest in women and people under 65.
  • 5. Seasonal variations influencing circadian One interesting observation from the behavior can be simulated by applying studies of entrainment by skeleton different experimental photoperiods. A photoperiods is the bistability photoperiod is described by the ratio of phenomenon. A full photoperiod will light to darkness during a 24-hour cycle. entrain the biological clock no matter Under laboratory conditions, summertime how short or long is the photoperiod, light conditions are typically represented i.e., the duration of the light portion by cycles of 18 hours light and 6 hours of the light-dark cycle. Thus LD 1:23, dark or of 14 hours light and 10 hours LD 3:21, LD 6:18, LD 8:16, LD 10:14, dark (LD 18:6 and LD 14:10, respectively), LD 12:12, LD 14:10, LD 16:8, LD 18:6, whereas winter light conditions are LD 21:3 and LD 23:1 are all equally mimicked by an LD 6:18 cycle or an LD likely to entrain a clock. On the other 10:14 cycle. In photoperiod experiments hand, with skeleton photocycles, the external time of the Zeitgeber rhythm photoperiod matters. The biological is specified as ExT (External Time) with clock quot;prefersquot; short photoperiods to ExT12 corresponding to the middle of the long photoperiods. Thus, when light-phase. Most laboratories use a rapid exposed to a skeleton photocycle that transition from light to dark and from attempts to entrain to a cycle dark to light and apply the same mimicking a long photoperiod, the wavelength range and light intensity rhythm will, instead, reverse the during the whole light period. However, quot;nightquot; and quot;dayquot; (often with an abrupt this does not truly reflect natural lighting phase-jump). conditions.
  • 6. From one to many A personal tribune 6
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  • 8. From one to many A personal tribune A personal tribune A personal tribune 8
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  • 10. From one to many Reader A personal tribune Reader A personal tribune A personal tribune Reader 10
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  • 12. From one to many Reader A personal tribune Reader A personal tribune A personal tribune Reader 12
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  • 14. From one to many Reader A personal tribune Reader A personal tribune Reader A personal tribune Reader 14
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  • 17. What does it mean for research? Certified knowledge, instruments Institutions, peers 17
  • 18. The Plant Cell, Vol. 17, 2856–2858, November 2005, www.plantcell.org ª 2005 American Society of Plant Biologists LETTER TO THE EDITOR A Toxic Mutator and Selection Alternative to the Non-Mendelian RNA Cache Hypothesis for hothead Reversion Lolle and colleagues observed frequent toxic and mutagenic. The HTH gene en- resulting in the enrichment of hth/HTH true reversion of hothead (hth) mutations codes a product whose closest character- zygotes because the reversion rate was of Arabidopsis thaliana, whereby up to 10% ized relative is an MBC oxidoreductase that much higher for pollen than for eggs (Figure of the progeny of self-pollinated homozy- hydrolyzes the aromatic mandelonitrile in 1B). Our selection hypothesis appears in- gous hth/hth mutants carried a grandpa- stone fruits (Zheng and Poulton, 1995) consistent with the reported 3:1 progeny rental HTH allele (Lolle et al., 2005). (Figure 1A). Arabidopsis has complex met- ratio from selfed heterozygotes because Instability was not limited to the HTH abolic pathways for the production of selection in favor of HTH pollen should de- gene: hth mutants displayed conversion glucosinolates (Wittstock and Halkier, crease the fraction of hth/hth progeny, but of genome-wide polymorphisms to the 2002; Brown et al., 2003), some of which HTH could have a paternal effect where an genotype of a recent ancestor. The possi- are aromatic and resemble mandelonitrile hth/HTH heterozygous anther provides its bility that a mutator phenotype caused (Figure 1), and aromatic glucosinolates and hth pollen with sufficient HTH enzyme indiscriminate changes, thereby increasing their derivatives are mutagenic (Musk et al., to avoid a crisis. An hth/hth anther would the reversion rate of hth, was discounted 1995; Kassie et al., 1999; Kassie and provide no enzyme. Selection favoring re- because reverted HTH alleles showed no Knasmuller, 2000; Canistro et al., 2004). vertant cells could also act in the shoot additional nucleotide changes, whereas 50 The sticky surface properties of the HTH apical meristem, in the flower meristem, to 100 changes per sequenced allele would phenotype, which suggest alterations of and in the anther primordia. In meristem be expected from the ;5% hth reversion cuticle, cell wall, and perhaps membranes, tissues, selection could be influenced by rate. These genetic instabilities were inter- might also be an effect of the toxic mutator. the defective cellular surface properties of preted as a memory of a past genotypic If an alternative genetic reservoir exists hth mutants that lead to postgenital organ state. A cache of double-stranded RNA and it restores mutations to the previous fusion (Lolle et al., 1998). Selection could from the previous genotype was proposed, genotype, it should be revised gradually also act on seed, decreasing germination which, at times of stress corrects mutated so that its memory should fade with cell of hth/hth zygotes in favor of HTH/hth sites in a template-directed manner. The divisions. Yet, data that addresses the individuals. existence of an alternate reserve genome reversion rate are available in a previous The precise reversion of hth mutations appears consistent with the data and would article by the same group and are inconsis- without the appearance of secondary mu- necessitate a revision of our theories of tent with the above expectation (Lolle et al., tations is consistent with a template-driven heredity. Two recent commentaries on this 1998). In complementation tests between repair but also with the alternative hypoth- discovery suggested that, instead of an hth alleles, wild-type plants were observed esis of mutagenesis and selection. As ex- RNA cache, the hth-correcting mechanism among the progeny of trans-heterozygotes plained above, any significant mutation depends on ectopic gene conversion and were thought to result from intragenic rate coupled to selection can yield frequent (Chaudhury, 2005) or on an elusive DNA recombination. These were almost certainly revertants, and the probability of finding cache (Ray, 2005). Thus, all explanations revertants and not recombinants. The hth- secondary mutations at HTH revertant offered until now invoke novel genetic 10/hth-8 trans-heterozygote produced 30 alleles is proportional to the mutation rate. phenomena. We offer an alternative expla- wild types among 1858 individuals, whereas In fact, the highest mutation rate compat- nation based on established genetic and hth-10/hth-4 produced only mutant prog- ible with survival is likely to be significantly evolutionary principles. HTH could be a meta- eny (n ¼ 1629) (Lolle et al., 1998; Krolikowski lower than the rates that would generate bolic enzyme whose impairment causes et al., 2003). The same alleles, hth-10 and frequent concurrent mutations on the HTH the accumulation of toxic and mutagenic hth-4, were reported to revert in the 2005 gene. We know from TILLING experiments compounds that act at random DNA sites. article and to do so through multiple gen- the genomic consequences of moderately The observed high reversion rate of hth erations (Lolle et al., 2005). Thus, the rate of intense mutagenesis: in Arabidopsis, it pro-
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  • 30. What does it mean for research? Certified knowledge, instruments Institutions, peers Training, incorporated Education skills system 30
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  • 33. What does it mean for research? Certified knowledge, instruments Institutions, peers Training, incorporated Education skills system Economic system Competitive advantage, innovation 33
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  • 37. What does it mean for research? Certified knowledge, instruments Institutions, peers Training, incorporated Education skills system Public Economic authorities system Collective goods, Competitive power, prestige, advantage, health, innovation 37 environment...
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  • 41. What does it mean for research? Certified knowledge, instruments Institutions, peers Training, Expertise, incorporated popularization Media, museums, Education skills public forums system Public Economic authorities system Collective goods, Competitive power, prestige, advantage, health, innovation 41 environment...
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  • 43. Percentage of science news in Belgian newspapers 20 15 10 5 0 Vif/L’Express J. du Mardi Le Soir Libre Belgique Tendance L’Echo Dernière heure http://www.belspo.be/belspo/home/publ/pub_ostc/Journ/rappULg_fr.pdf
  • 44. Content of these science news Technology Medicine Science http://www.belspo.be/belspo/home/publ/pub_ostc/Journ/rappULg_fr.pdf
  • 45. Do you prefer that science information is presented to you… Other Scientists Journalists Special Eurobarometer 282, December 2007, p. 40
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  • 48. What could keep you from blogging • Internally – time – hot science 48
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  • 50. What could keep you from blogging • Internally – time – hot science – debating 50
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  • 52. What could keep you from blogging • Internally – time – hot science – debating • Externally – being scooped 52
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  • 54. What could keep you from blogging • Internally – time – hot science – debating • Externally – being scooped – lack of recognition – lack of visibility 54
  • 58. The landscape of science blogs • Communities, agregators 58
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  • 64. The landscape of science blogs • Communities, agregators • Rankings 64
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  • 67. The landscape of science blogs • Communities, agregators • Rankings • Diversity – scientists – medicine doctors – journalists – engineers – students – teachers – amateurs 67
  • 68. Nine commandments before you start • take your time • be yourself • match the form and the content • write for everyone • be transparent • offer some eye candy • be creative • foster comments • have fun! 68