tag:blogger.com,1999:blog-59161217426427614502024-03-18T02:48:28.065-07:00Of Bacteria and MenMaintained by Robin Tecon. This blog is about bacteria (and other microbes) and the scientists who study them.Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.comBlogger66125tag:blogger.com,1999:blog-5916121742642761450.post-75007390974582547622021-02-07T07:28:00.000-08:002021-02-07T07:28:12.016-08:00The quiet revolution of Oswald Avery<p> <table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;"><tbody><tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-huly3BMPXQo/YCAEWKFrixI/AAAAAAAADC8/mPNUBjjHdCYAd-_suNQuop6sXnkZ9J2PACLcBGAsYHQ/s948/Avery_in_his_lab__1948__is_inscribed_to_his_associate__Dr._Bertram_Sprofkin.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="777" data-original-width="948" src="https://1.bp.blogspot.com/-huly3BMPXQo/YCAEWKFrixI/AAAAAAAADC8/mPNUBjjHdCYAd-_suNQuop6sXnkZ9J2PACLcBGAsYHQ/s320/Avery_in_his_lab__1948__is_inscribed_to_his_associate__Dr._Bertram_Sprofkin.jpg" width="320" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Avery in his lab, 1948. Source: <a href="https://digitalcommons.rockefeller.edu/faculty-members/7/" target="_blank">Rockefeller Archive</a><br /></td></tr></tbody></table><br /><!--[if gte mso 9]><xml>
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</p><p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">Imagine a
world where we build skyscrapers more than 300 meters high, where we know of
nuclear fission, where the first digital computers have been designed, where the
first color television has been produced, but a world where we do not even know<i>
what stuff genes are made of</i>! [1] This is the world of the early 1940s,
before Oswald Avery achieved his ‘<i>quiet revolution’</i> – to borrow an
expression from the biologist and author <a href="https://en.wikipedia.org/wiki/Matthew_Cobb" target="_blank">Matthew Cobb</a> <span style="mso-spacerun: yes;"> </span></span><a href="https://www.theguardian.com/science/blog/2013/jun/03/oswald-t-avery-genetic-science-dna" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">on the subject</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;">. </span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">I knew of
Avery and his experiments – as do all microbiologists – from the textbooks and
microbiology class: working on pneumococci, Avery showed in 1944 that the
active compound in bacterial transformation was DNA. In that he was providing
an explanation to the illustrious findings of </span><a href="https://en.wikipedia.org/wiki/Griffith%27s_experiment" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">Griffith</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;"> in the late 1920s, who demonstrated that, in
infected mice, avirulent mutants of <i>Streptococcus pneumoniae</i> could be
effectively <i>transformed</i> into the deadly kind via an unknown process involving
contact with heat-killed virulent cells (again, textbook knowledge).</span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">Alas,
textbooks usually fail to convey much excitement about such groundbreaking
episodes of human inquiry. To be fair, this is of course not the textbooks’ mission.
This said, I can’t remember that my microbiology class fared much better in
that task – often the amount of material to be covered in class does not allow
for much dwelling into the historical context. </span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">So I was
thrilled to (re)discover the story of Avery in Cobb’s excellent book, </span><a href="https://www.sciencefactory.co.uk/matthew-cobb">Life's Greatest Secret:
The Race to Crack the Genetic Code</a><cite><span style="font-family: "Calibri",sans-serif; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;"> </span></cite><cite><span lang="EN-US" style="font-family: "Calibri",sans-serif; font-style: normal; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;">(2015),
which explores in depth the work that led to the resolution of the DNA
structure and later to the deciphering of the genetic code. Cobb spends a whole
chapter on Avery’s work and life, and brings to light many fascinating aspects.
</span></cite></p>
<p class="MsoNormal"><cite><span lang="EN-US" style="font-family: "Calibri",sans-serif; font-style: normal; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;">The career of Oswald T. Avery </span></cite>(1877-1955)<span lang="EN-US" style="mso-ansi-language: EN-US;"> centered in the study of pneumonia
bacteria and the immunological response they elicit. We have to remember that,
before antibiotics became widespread, pneumonia was among the deadliest
infectious diseases in the world [sadly we should also stress that millions of
people still die of pneumonia </span><a href="https://ourworldindata.org/pneumonia#burden-of-pneumonia"><span lang="EN-US" style="mso-ansi-language: EN-US;">every year</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;">, although this number is
decreasing]. Avery had joined the </span><a href="https://www.rucares.org/"><span lang="EN-US" style="mso-ansi-language: EN-US;">Rockefeller Institute Hospital</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;"> in New York in 1913 in order to
pursue this research, with the goal of developing therapies against pneumococcus.
He stayed at Rockefeller thirty years, until his retirement in 1943.</span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">Avery was
interested in why certain pneumococci are more virulent than others. In the
1920s, he found that virulent strains typically embed themselves within a large
polysaccharidic capsule that protects them from the human body’s defenses. In
1928, in London, Fred Griffith found that pneumonia bacteria devoid of capsule
could be transformed into virulent ones producing capsules, simply by putting
them into contact with dead capsule-producing bacteria. But what was the
process? Griffith thought incorrectly that the avirulent bacteria were using
the capsules of the dead virulent bacteria as a template to make new ones. </span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">From the
early 1930s, Avery worked to isolate what they called ‘<i>the transforming
principle’</i> from cultures of pneumococci, and to identify its chemical
nature, with the help of the Canadian scientist Colin MacLeod. They managed
this feat by using a messy, dangerous procedure with a commercial kitchen cream
separator that leaked and produced tons of aerosols – I kid you not. They also
found that calcium chloride precipitated nucleic acids into a white, gooey
substance (if you have done DNA extraction you know how that looks like). The
white precipitate, which contained nucleic acids and polysaccharides, was very
potent in transforming bacteria, as demonstrated by MacLeod, who had to leave
the lab in 1941.</span></p><p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;"> <table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto;"><tbody><tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-CCeF62JT7hE/YCAE8-bHbJI/AAAAAAAADDE/7WfShbNLNksBB5f64tKiULoLZH75ttH0gCLcBGAsYHQ/s2048/avery_lab__circa_1920scrN.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1506" data-original-width="2048" src="https://1.bp.blogspot.com/-CCeF62JT7hE/YCAE8-bHbJI/AAAAAAAADDE/7WfShbNLNksBB5f64tKiULoLZH75ttH0gCLcBGAsYHQ/s320/avery_lab__circa_1920scrN.jpg" width="320" /></a></td></tr><tr><td class="tr-caption" style="text-align: center;">Avery lab around 1920. Source: <a href="https://digitalcommons.rockefeller.edu/laboratories-and-equipment/11/" target="_blank">Rockefeller Archive</a><br /></td></tr></tbody></table><br /> </span><span lang="EN-US" style="mso-ansi-language: EN-US;">At that
time another young researcher joined the Avery lab. His name was Maclyn
McCarthy, and he made a decisive contribution by showing that the polysaccharides
could be enzymatically digested in the precipitate without it losing its
transforming ability. It became increasingly clear that most of the transforming
precipitate was made of DNA. What is more, some enzymes active on DNA were able
to block transformation. </span>
</p><p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">This should
have been the nail in the coffin of that story, however, resistance to grant
DNA that extraordinary role was strong: DNA shows no variation whatsoever, how
could it be the transforming principle? Proteins are varied and very low
amounts show activity – surely they are the <i>stuff</i> responsible for
transformation. And you can never be sure that your precipitate is totally protein-free!</span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">So while all
the evidence pointed at DNA as the agent of transformation, many were still
convinced that it could not be – a powerful expectation bias that complicated
the acceptance of Avery’s work. He and his team continued to work tirelessly to
strengthen the case for DNA. Avery noted, in a letter to his brother:</span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="mso-ansi-language: EN-US;"></span></i></p><blockquote><i>‘We have
isolated highly purified substance of which as little as 0.02 of a microgram is
active in inducing transformation… this represents a dilution of 1 part in a
hundred million – potent stuff that – and highly specific. This does not leave
much room for impurities – but the evidence is not good enough yet.’</i></blockquote><p></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">In 1943,
Avery proposed the connection between DNA and genes. He had not solved the
problem of protein impurities – after all, you cannot prove a negative – but at
that time the attitude towards DNA was changing, weakening the opposition to
its role. Avery started to write down all their results, a pile of evidence
from different types of experiments. He wrote in that paper:</span></p>
<p class="MsoNormal"><i><span lang="EN-US" style="mso-ansi-language: EN-US;"></span></i></p><blockquote><i>‘The
inducing substance has been likened to a gene, and the capsular antigen which
is produced in response to it has been regarded as a gene product.’</i></blockquote><p></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">The paper,
authored by Avery, McLoed and McCarthy, was published in February 1944 in the <i>Journal
of Experimental Medicine</i>. Its initial reception by the scientific community
was good and, in the next couple of years, Avery and McCarthy continued to publish,
adding more evidence to their case. Avery received the Gold Medal of the New York
Academy of Medicine. Erwin Chargaff, inspired by Avery, started to study DNA
composition. In 1945, André Boivin at the Institut Pasteur demonstrated
transformation in <i>E. coli</i>, supporting Avery’s findings on the importance
of DNA. </span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;">After 30
years of hard work, the quiet revolution was very much underway. <cite><span style="font-family: "Calibri",sans-serif; font-style: normal; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;">Avery received many awards
for his work on pneumococcus, albeit never the Nobel Prize... </span></cite></span></p><p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;"><cite><span style="font-family: "Calibri",sans-serif; font-style: normal; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;">Reference: Cobb, Matthew. (2015) </span></cite></span><span lang="EN-US" style="mso-ansi-language: EN-US;"><cite><span style="font-family: "Calibri",sans-serif; font-style: normal; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;"><a href="https://www.sciencefactory.co.uk/matthew-cobb">Life's Greatest Secret:
The Race to Crack the Genetic Code.<span style="color: black;"> <span style="color: white;">Basic Books, 464 pages.</span></span></a><cite><span style="font-family: "Calibri",sans-serif; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;"></span></cite> </span></cite></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"> </span>[1] <cite><span style="font-family: "Calibri",sans-serif; font-style: normal; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;">In 1933,
Thomas Hunt Morgan noted, during his Nobel Prize acceptance lecture: </span></cite><cite><span style="font-family: "Calibri",sans-serif; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;">‘There is no consensus of opinion amongst
geneticists as to what the genes are – whether they are real or purely
fictitious.’</span></cite></span></p><p class="MsoNormal"><span lang="EN-US" style="mso-ansi-language: EN-US;"><cite><span style="font-family: "Calibri",sans-serif; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-theme-font: minor-bidi; mso-hansi-theme-font: minor-latin;"><br /></span></cite><cite><span style="font-family: "Calibri", sans-serif;"></span></cite></span></p>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com1tag:blogger.com,1999:blog-5916121742642761450.post-91253707329190538152019-03-10T08:06:00.004-07:002021-02-07T08:03:26.828-08:00A view of microbial life in soil<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://2.bp.blogspot.com/-x8B-VGGegn4/XIUL7QaQcBI/AAAAAAAABTo/osv_QOt9THYMB2Vtjdf0f4QG7Vu_GcnuQCLcBGAs/s1600/Microbial_Life_in_Soil_3.tif" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="864" data-original-width="1139" height="301" src="https://2.bp.blogspot.com/-x8B-VGGegn4/XIUL7QaQcBI/AAAAAAAABTo/osv_QOt9THYMB2Vtjdf0f4QG7Vu_GcnuQCLcBGAs/s400/Microbial_Life_in_Soil_3.tif" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="http://www.step.ethz.ch/research/active-projects/microbial-life-in-porous-media/erc-advanced-grant-soillife/gallery.html" target="_blank">Image source</a></td></tr>
</tbody></table>
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All soils teem with microscopic life that is invisible to the naked eye, and for that reason often overlooked. Yet, microorganisms are an essential component of all soils, and through their metabolic activity (mineral weathering, production and recycling of organic matter, and more) soil microbes actually play a major role in soil formation, development, and fertility.<br />
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The images presented here show diverse microorganisms inhabiting a pasture soil. I sampled this soil on the <a href="https://www.uetliberg.ch/de/willkommen" target="_blank">Uetliberg</a>, in Zürich, Switzerland, in 2018. Samples were chemically fixed and observed with scanning electron microscopy. Post-acquisition pseudocoloring was applied to the images - in other words, colors were added to the original black and white images to facilitate visualization of the microbes and soil particles. (The pseudocolors do not represent the real colors of the samples.)<br />
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All images are courtesy of the <a href="http://www.step.ethz.ch/" target="_blank">Soil and Terrestrial Environmental Physics</a> group of Dani Or at ETH Zurich. SEM image acquisition and coloring by Anne Greet Bittermann, ETH Zurich - <a href="http://www.scopem.ethz.ch/" target="_blank">ScopeM</a>.<br />
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<div class="separator" style="clear: both; text-align: center;">
<a href="https://3.bp.blogspot.com/-YbIPBz2eWzw/XIUhyfc09kI/AAAAAAAABUA/bu2T1OIiEjcVhjkJQTB2ByhCoAuqb0zngCLcBGAs/s1600/Microbial_Life_in_Soil_5.png" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="470" data-original-width="700" height="267" src="https://3.bp.blogspot.com/-YbIPBz2eWzw/XIUhyfc09kI/AAAAAAAABUA/bu2T1OIiEjcVhjkJQTB2ByhCoAuqb0zngCLcBGAs/s400/Microbial_Life_in_Soil_5.png" width="400" /></a></div>
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We do not know the precise identity of these microbes (we would need DNA sequencing for that), but given their shape and size some level of characterization is possible. Most of them are bacteria, which are the most abundant cellular organisms in all soils.<br />
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<a href="https://3.bp.blogspot.com/-lUfalYVWnLc/XIUi_sh6IyI/AAAAAAAABUI/uXPyl0KAGUoLXmXxPXMWD9Vl7ffvHzjEgCLcBGAs/s1600/Microbial_Life_in_Soil_4.tif" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="949" data-original-width="1151" height="328" src="https://3.bp.blogspot.com/-lUfalYVWnLc/XIUi_sh6IyI/AAAAAAAABUI/uXPyl0KAGUoLXmXxPXMWD9Vl7ffvHzjEgCLcBGAs/s400/Microbial_Life_in_Soil_4.tif" width="400" /> </a></div>
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<div class="separator" style="clear: both; text-align: left;"><span><a name='more'></a></span> </div><div class="separator" style="clear: both; text-align: left;">Scanning electron microscopy reveals the complex arrangements of bacterial cells and soil particles with a great level of details. The colored filaments are likely remnants of <a href="https://en.wikipedia.org/wiki/Extracellular_polymeric_substance" target="_blank">extracellular polymeric subtances</a> connecting cells and soil together. </div>
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<a href="https://3.bp.blogspot.com/-JtqHHScjt48/XIUjwoor_II/AAAAAAAABUQ/SYx8he_M7tgqz32I7TsA5m_0NL3N4K2TgCLcBGAs/s1600/Microbial_Life_in_Soil_1.tif" style="margin-left: 1em; margin-right: 1em;"><img border="0" data-original-height="847" data-original-width="1205" height="280" src="https://3.bp.blogspot.com/-JtqHHScjt48/XIUjwoor_II/AAAAAAAABUQ/SYx8he_M7tgqz32I7TsA5m_0NL3N4K2TgCLcBGAs/s400/Microbial_Life_in_Soil_1.tif" width="400" /></a></div>
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Those images (and more) can be downloaded from our <a href="http://www.step.ethz.ch/research/active-projects/microbial-life-in-porous-media/erc-advanced-grant-soillife/gallery.html" target="_blank">image gallery</a>. </div>
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For those interested in soil microbial life, we published an <a href="https://academic.oup.com/femsre/article/41/5/599/4082850" target="_blank">open access review </a>on that topic in the journal FEMS Microbiology Reviews. <br />
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<br />Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com3tag:blogger.com,1999:blog-5916121742642761450.post-84907246349854219482018-07-22T03:02:00.005-07:002021-02-07T08:01:41.928-08:00Self-organization of bacterial populations<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://3.bp.blogspot.com/-L_G4awWBA74/W1HQ8hr1YPI/AAAAAAAABLw/5okNC_8LeW4YtZ7Grmy9V6hjW2DGMejWgCLcBGAs/s1600/PputidaPveroni.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="398" data-original-width="565" height="280" src="https://3.bp.blogspot.com/-L_G4awWBA74/W1HQ8hr1YPI/AAAAAAAABLw/5okNC_8LeW4YtZ7Grmy9V6hjW2DGMejWgCLcBGAs/s400/PputidaPveroni.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Fluorescent bacteria in glass microchannels</td></tr>
</tbody></table>
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In many environments, hundreds, sometimes thousands of different microbial species coexist as mixtures of cells of various sizes and shapes. For example, each human being teems with their very own and unique microbial mixture (trillions of cells), as <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564958/" target="_blank">the human microbiome project unveiled </a>a few years ago. <a href="https://academic.oup.com/femsre/article/41/5/599/4082850" target="_blank">Microbial diversity in soil </a>is equally<span face=""calibri" , "sans-serif"" style="font-size: 11pt; line-height: 115%;"> –</span> possibly even more<span face=""calibri" , "sans-serif"" style="font-size: 11pt; line-height: 115%;"> – </span>astounding, with a gram of rich soil capable to host thousands to millions of distinct bacterial and archaeal species, as well as hundreds of fungal and protistan species. A <a href="https://www.nature.com/articles/nature24621" target="_blank">recent study </a>in the magazine <i>Nature </i>highlights the results of the <a href="http://www.earthmicrobiome.org/" target="_blank">earth microbiome project</a>, which aims at revealing the extent of microbial diversity on our planet.<br />
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<br />
<span lang="EN-US" style="mso-ansi-language: EN-US;">Yet, despite this wealth of
diversity, microbial communities are not simply soups of species – there is
order hiding behind this curtain of complexity. Actually, the more we look, the
more we find <i>patterns </i>of microbial organization in the natural world. Some
patterns are obvious and have been known for a long time, such as the distinct
layers of microorganisms visible with the naked eye in </span><a href="http://aem.asm.org/content/73/9.cover-expansion" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">sections of microbial mats</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;">. The vast majority of patterns, however, reveal themselves only at the
scale of individual microbes, that is, at the microscopic scale. See, for
example, the beautiful arrangements revealed in the </span><a href="http://www.mbl.edu/jbpc/staff/jmarkwelch/" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">lab of Jessica Mark Welch </span></a><span lang="EN-US" style="mso-ansi-language: EN-US;">at the University of Chicago. </span><br />
<span lang="EN-US" style="mso-ansi-language: EN-US;"><br />
Microbial populations are thus often spatially organized at small scale, and in
a very defined and refined way. But how does it work? Obviously, microbes don't
organize following some kind of blueprint that is imposed on the community!...
But what then? Part of the answer seems to reside in so-called </span><a href="https://en.wikipedia.org/wiki/Self-organization" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">self-organization</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;"> processes. With such processes, patterns emerge from the individual
behavior of cells that can only sense the conditions in their local environment
and react accordingly. This in appearance simple process at the individual
level can lead to seemingly complex patterns of organization at larger scale.
Think of </span><a href="https://www.mnn.com/earth-matters/animals/stories/the-incredible-science-behind-starling-murmurations" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">bird murmuration</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;">, or of how </span><a href="https://www.princeton.edu/news/2015/11/30/ants-build-living-bridges-their-bodies-speak-volumes-about-group-intelligence" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">ants can form bridges </span></a><span lang="EN-US" style="mso-ansi-language: EN-US;">with their own bodies! I also discussed spatial patterns of bacterial
organization triggered by metabolic cooperation </span><a href="http://ofbacteriaandmen.blogspot.ch/2017/03/cooperation-shapes-spatial-patterns-of.html" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">in a previous post</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;">. </span><br />
<br />
<span lang="EN-US" style="mso-ansi-language: EN-US;">In </span><a href="https://www.nature.com/articles/s41467-018-03187-y" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">a recent paper</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;">
whose lead author is my colleague </span><a href="http://www.step.ethz.ch/people/phd-students/benedict-borer.html" target="_blank"><span lang="EN-US" style="mso-ansi-language: EN-US;">Benedict Borer</span></a><span lang="EN-US" style="mso-ansi-language: EN-US;">,
we examined some of the basic processes that can lead to bacterial spatial
self-organization. (In that study we were specifically interested in pore
networks that mimic the spatial structure of soil aggregates, but the processes
that matter here are valid in other kinds of environments as well.) The idea is as
follows. In a given habitat, bacterial populations with distinct metabolic
capabilities and food preferences would spontaneously arrange in space in order
to optimize their use of the available resources. We thought there must be two
necessary conditions for that. First, that the bacterial cells have some level
of motility (which could be flagellar motility, such as swimming, or simply
movement provide by growth and cell division). Second, that gradients of carbon
and nutrients are present in the habitat (i.e. there must be some spatial
heterogeneity for the microbes to respond to). </span><br />
<br />
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<span lang="EN-US" style="mso-ansi-language: EN-US;">We chose to work with two
bacterial species that differ on their ability to respire: one is a strict
aerobe (<i>Pseudomonas putida</i>), which only respires using oxygen as final
electron acceptor, while the other (<i>Pseudomonas veronii</i>) is a
facultative anaerobe that can respire with oxygen but also with nitrate as
final electron acceptor. Both species are motile thanks to flagella that they
can use to swim within liquid films. To facilitate observation, the two species
were each tagged with a distinct fluorescent protein (green or red). The two
bacterial populations were inoculated into micrometric pore networks with
various structures, and which allowed us to create gradients of oxygen
(coming from the periphery of the network) and of carbon source (citrate,
coming from the center of the network). Although initially well-mixed in the
center of the network, after a week of incubation the two bacterial species
segregated in the network to form two distinct and coexisting populations (see
figure below). One grew preferentially where the oxygen was more abundant (the obligate aerobe), while the other could occupy the anoxic niche at the center of the network, which also contained more carbon.</span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://4.bp.blogspot.com/-lKwrS1WxX6o/W1RTq6Qts2I/AAAAAAAABMc/zorRSo188CAODB2q1Ads8xo8gpg_RJAwQCLcBGAs/s1600/41467_2018_3187_Fig3.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="351" data-original-width="900" height="155" src="https://4.bp.blogspot.com/-lKwrS1WxX6o/W1RTq6Qts2I/AAAAAAAABMc/zorRSo188CAODB2q1Ads8xo8gpg_RJAwQCLcBGAs/s400/41467_2018_3187_Fig3.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><span style="font-size: small;"><span style="font-family: "times" , "times new roman" , serif;">The two bacterial populations, initially well-mixed, grow and segregate in the pore network as function of their respiration metabolism. <a href="https://www.nature.com/articles/s41467-018-03187-y" target="_blank">From Borer et al., 2018</a></span></span></td><td class="tr-caption" style="text-align: center;"></td><td class="tr-caption" style="text-align: center;"></td></tr>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">Interestingly, this spatial
organization did not occur when carbon source and oxygen were provided together
(i.e., there was no counter-gradients of oxygen and carbon). Another intriguing
result was that the coexistence of the two species, as seen in the figure,
could not been achieved in well-mixed liquid environments (vials or flasks),
because one of the species would always win over and dominate the community (see below).
This illustrates how the habitat spatial structure can help limit competition
and maintain species coexistence.</span><br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://2.bp.blogspot.com/-M-TrlxIYp_o/W1RYVv6TN_I/AAAAAAAABMo/CL4dcwxnCSox6e6vgb4e2rsEbzTs1x7XgCLcBGAs/s1600/41467_2018_3187_Fig5.jpg" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="307" data-original-width="900" height="136" src="https://2.bp.blogspot.com/-M-TrlxIYp_o/W1RYVv6TN_I/AAAAAAAABMo/CL4dcwxnCSox6e6vgb4e2rsEbzTs1x7XgCLcBGAs/s400/41467_2018_3187_Fig5.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Experimental and modeling results show competitive exclusion in homogeneous cultures (a) and coexistence in structured pore networks (b). The percentage corresponds to the connectivity in the network (100% is highest connectivity).</td></tr>
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<![endif]--><span style="font-size: small;"><span style="font-family: "times" , "times new roman" , serif;"><span lang="EN-US" style="line-height: 115%;">Admittedly, our system is artificial and our
community only composed of two species... Yet, the basic mechanisms that we observed most
probably also apply to more complex environments and could participate to the
final structure of the community. Bacteria have a remarkable faculty of optimizing their distribution and activity in complex habitats, which we could demonstrate with our simple mathematical and experimental models.</span></span></span> </span><br />
<span lang="EN-US" style="mso-ansi-language: EN-US;">
</span><br />
<span face=""calibri" , "sans-serif"" style="font-size: small; line-height: 115%;"><span style="font-size: x-small;"><span style="font-family: "times" , "times new roman" , serif;"><br /></span></span></span>
<span><a name='more'></a></span><span><!--more--></span>Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com13tag:blogger.com,1999:blog-5916121742642761450.post-9794082906218609622017-09-17T09:23:00.002-07:002018-07-22T03:19:28.635-07:00The Vital Question, by Nick Lane - Part 2<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://4.bp.blogspot.com/-c_UEW62diZA/Wb1I5JHDzqI/AAAAAAAAA6c/yHosv3vicSoeKvd9iE1p3t_vfnihdOmjwCLcBGAs/s1600/Mitochondrion_186.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" data-original-height="189" data-original-width="186" height="320" src="https://4.bp.blogspot.com/-c_UEW62diZA/Wb1I5JHDzqI/AAAAAAAAA6c/yHosv3vicSoeKvd9iE1p3t_vfnihdOmjwCLcBGAs/s320/Mitochondrion_186.jpg" width="314" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Mitochondrion. Source: <a href="https://commons.wikimedia.org/wiki/File:Mitochondrion_186.jpg" target="_blank">US NIH</a></td></tr>
</tbody></table>
<blockquote class="tr_bq">
<i>" So what about sex, or the nucleus, or phagocytosis? [...] If each of these traits arose by natural selection <span lang="EN-US" style="font-family: "calibri" , "sans-serif"; font-size: 11.0pt; line-height: 115%;">– </span>which they undoubtedly did <span lang="EN-US" style="font-family: "calibri" , "sans-serif"; font-size: 11.0pt; line-height: 115%;">–</span> and all of the adaptive steps offered some small advantage <span lang="EN-US" style="font-family: "calibri" , "sans-serif"; font-size: 11.0pt; line-height: 115%;">–</span> which they undoubtedly did <span lang="EN-US" style="font-family: "calibri" , "sans-serif"; font-size: 11.0pt; line-height: 115%;">–</span> then we should see multiple origins of eukaryotic traits in bacteria. But we don't. This is little short of an evolutionary 'scandal'. "</i><!--[if gte mso 9]><xml>
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Nick Lane <!--[if gte mso 9]><xml>
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</xml><![endif]--><span lang="EN-US" style="font-family: "calibri" , "sans-serif"; font-size: 11.0pt; line-height: 115%;">–</span> <a href="http://nick-lane.net/books/the-vital-question-why-is-life-the-way-it-is/" target="_blank">The Vital Question</a> (2015)</blockquote>
<br />
In my <a href="https://ofbacteriaandmen.blogspot.ch/2017/07/the-vital-question-by-nick-lane.html" target="_blank">previous post</a> I commented on the first part of Nick Lane's book, which deals with the proton-motive force and the origin of life. This second post focuses on the second half of the book, which explores the origin of complex life (i.e. eukaryotic cells).<br />
<br />
If the first half of the book was equally part history of the field and part new hypotheses, the second half leans clearly more towards hypothetical ideas <!--[if gte mso 9]><xml>
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</xml><![endif]--><span lang="EN-US" style="font-family: "calibri" , "sans-serif"; font-size: 11.0pt; line-height: 115%;">–</span> albeit including many facts, and backed with rigorous thinking. Lane's big idea is the following. Most traits that differentiate eukaryotes from prokaryotes (cell and genome sizes, nucleus, introns, sexual reproduction) ultimately follow from a single and singular event: the endosymbiosis event that created mitochondria. For Lane, the organelles that power respiration in all eukaryotic cells are the one special ingredient that permitted the development of cellular complexity.<br />
<br />
<a name='more'></a><br /><br />
Thanks mostly to <a href="https://ofbacteriaandmen.blogspot.ch/2012/06/endosymbiotic-theory-of-lynn-margulis.html" target="_blank">Lynn Margulis</a>, we know now that at the origin of mitochondria lies the symbiosis of bacteria with an ancestor cell; the resulting 'symbiogenesis' gave birth to the eukaryotic cell. We do not know exactly who the ancestor cell was, although it is quite sure that it was more related to archaea than to bacteria (see for example this recent <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571572/" target="_blank">article </a>by <a href="https://ofbacteriaandmen.blogspot.ch/2012/09/the-logic-of-chance-by-eugene-koonin.html" target="_blank">Eugene Koonin</a>). What is puzzling, Koonin notes, is that comparative genomics indicates that the last common ancestor of all eukaryotes already possessed most of the signature traits of modern eukaryotes, including mitochondria, a nucleus, an endoplasmic reticulum and a cytoskeleton. You don't find intermediates between pro- and eukaryotes with just one or a few of those features [1]. Lane also points at this curious fact in his book (p. 43):<br />
<br />
<blockquote class="tr_bq">
<i>"But where did all these parts come from? The eukaryotic common ancestor might as well have jumped, fully formed, like Athena from the head of Zeus. We gain little insight into traits that arose before the common ancestor <span lang="EN-US" style="font-family: "calibri" , "sans-serif"; font-size: 11.0pt; line-height: 115%;">–</span> essentially all of them.[...] There are no known evolutionary intermediates between the morphologically simple state of all prokaryotes and the disturbingly complex common ancestor of eukaryotes. All these attributes of complex life arose in a phylogenetic void, a black hole at the heart of biology."</i></blockquote>
<br />
This is the 'evolutionary scandal' that Lane was alluding to in the quote opening this post. Can we stifle this scandal? Lane believes so. And the answer to the 'black hole at the heart of biology' could be the mitochondrion, and more particularly the energy gain that it represents for the cell, as Lane and his colleague Bill Martin proposed a few years ago (<a href="http://www.nature.com/nature/journal/v467/n7318/full/nature09486.html?foxtrotcallback=true" target="_blank">Lane & Martin, <i>Nature </i>2010</a>). Without this initial energy boost, there would have been no possibility to evolve those unique eukaryotic features, such as larger size and complex intracellular structures.<br />
<br />
Take a cell's size, for example: the size of an eukaryotic cell is typically tens to hundreds of times larger than that of a prokaryotic cell. Why is it that bacteria do not form larger cells? Actually, some of them do: so-called giant bacteria exist, such as <i>Epulopiscium fishelsoni </i>(a long rod of 600 microns) and <i>Thiomargarita namibiensis </i>(a sphere almost 1 millimetre in diameter), but they are rare and grow slowly. They are also genetically very different from other bacteria in the sense that they show extreme polyploidy (respectively 200,000 and 18,000 genome copies in one cell!); these multiple genomes are not randomly distributed in the cell volume, but typically located close to the cell's membrane. As Lane and Martin suggest, this exteme number of genomes and their location is required to compensate for the extra size: genes required for energy production must be physically close to the membrane, hence if you have a vast volume and surface area, you need more copies of those genes (or genomes).<br />
<br />
Mitochondria permit to eschew the problem faced by giant bacteria: a eukaryotic cell contains thousands of them (1-2,000 in a human liver cell, and up to 300,000 in some large amoebae), and all those mitochondria contain a small genome (16 kb) encoding 13 key proteins of the respiratory chains (but not all: others, including the ATP synthase, are encoded in the nucleus). In the evolutionary history of mitochondria, this suggests that most of the original endosymbiont genes migrated to the genome of the host cell, while a few key genes remained associated to the mitochondrion, forming a microgenome. To Lane, the maintenance of those genes is dictated by energetics: these genes need to be close to the bioenergetic membranes for them to function properly. When these genes are mutated (like in some mitochondrial diseases), this has serious consequences for respiration. To conclude, mitochondria (and their small genome) offer a solution to complexity that is unavailable to bacteria as well as giant bacteria. Lane notes (p.189):<br />
<blockquote class="tr_bq">
<i>"There is no benefit in terms of energy per gene from becoming larger, except when large size is attained by endosymbiosis." </i></blockquote>
This concept of 'energy per gene' is at the core of the argument made by Lane and Martin. Endosymbiosis (ancestor mitochondria) was the innovation permitting to vastly increase the energy supply available per gene in the cell. This paved the way for the expression of a wider variety of proteins, followed by the evolution of other eukaryotic traits. Much more is discussed in Lane's fascinating book, such as the evolution of introns and the nucleus, or the evolution of apoptosis, but I will not discuss it here.<br />
<br />
I find Lane's ideas exciting and truly stimulating. It's important to note, however, that those ideas are not necessarily the final word on this discussion. Some biologists strongly disagree with the 'mitonchondrion-first' hypothesis for the evolution of complexity. Notably, Austin Booth and Ford Doolittle (<a href="http://www.pnas.org/content/112/33/10278.abstract" target="_blank">PNAS 2015</a>) at Dalhousie University (Canada), and Michael Lynch and Georgi Marinov (<a href="http://www.pnas.org/content/112/51/15690.abstract" target="_blank">PNAS 2015</a>) at Indiana University (USA). I let the curious reader discover for herself the arguments of these authors, as well as the rebuttal proposed by Lane and Martin (that you can find in the 'related content' of those articles). Scientific controversy and debate is doing well, and that's great news!<br />
<br />
The Vital Question is definitely a read worth your time! But in any case, a good way to start is by watching the lecture that Lane gave as a recipient of the Michael Faraday Prize. This sums up his views nicely.<br />
<br />
<div class="separator" style="clear: both; text-align: center;">
<iframe allowfullscreen="" class="YOUTUBE-iframe-video" data-thumbnail-src="https://i.ytimg.com/vi/PhPrirmk8F4/0.jpg" frameborder="0" height="266" src="https://www.youtube.com/embed/PhPrirmk8F4?feature=player_embedded" width="320"></iframe></div>
<br />
<br />
<u>Notes</u><br />
[1] One nuance can be brought here. As Lane reports, the group known as the archezoa were long thought to be such kinds of intermediates, since they do not possess mitochondria. However, mounting evidence suggest that archezoa derive from eukaryotes which lost mitochondria, not a missing link between prokaryotes and eukaryotes.<br />
<br />
<u>References</u><br />
<ul>
<li><span lang="EN-US">Lane, N. (2015) <i><a href="http://nick-lane.net/books/the-vital-question-why-is-life-the-way-it-is/" target="_blank">The Vital Question</a>.</i> Profile Books, London. Paperback edition (2016), 360 p.</span></li>
<li><span lang="EN-US">Lane, N., and W. Martin (2010) <a href="http://www.nature.com/nature/journal/v467/n7318/full/nature09486.html?foxtrotcallback=true" target="_blank">The energetics of genome complexity</a>. <i>Nature </i><b>467 </b>pp.929-934. </span> </li>
</ul>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com4tag:blogger.com,1999:blog-5916121742642761450.post-33898516364589220532017-07-09T03:11:00.000-07:002018-07-22T03:21:16.618-07:00The Vital Question, by Nick Lane<!--[if gte mso 9]><xml>
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<blockquote class="tr_bq">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US">“In
the end, respiration and burning are equivalent; the slight delay in the middle
is what we know as life.”</span></i></blockquote>
</div>
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<span lang="EN-US">This quote, from
<a href="http://nick-lane.net/about/" target="_blank">Nick Lane</a>’s book <i style="mso-bidi-font-style: normal;"><a href="http://nick-lane.net/books/the-vital-question-why-is-life-the-way-it-is/" target="_blank">The Vital Question</a> </i>(2015), is both poetic and true, which is the mark of great popular science writing.
What Lane’s book attempts to do (and in my opinion succeeds in doing) is to
radically change our perspective on life by showing us the crucial role played
by energy. </span></div>
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<br />
<span lang="EN-US">Lane is a biochemist at University College
London and already the author of <a href="http://nick-lane.net/books/" target="_blank">three books</a>. I think there’s something to be
said about popular science written by scientists, as opposed to science
journalists, in the sense that they can sometimes achieve much more than
educating. For example, they can <i style="mso-bidi-font-style: normal;">fundamentally</i>
change our understanding of some topics (that certainly happened to me on some occasions). Actually, reading <i style="mso-bidi-font-style: normal;">The Vital Question</i> reminded me of reading Richard Dawkins’ <i style="mso-bidi-font-style: normal;">The Selfish Gene </i>many years ago, and Lane’s
book did for me with biochemistry what Dawkins did with genetics and evolutionary
theory: it opened a window into a fascinating new landscape. </span><br />
<br />
<a name='more'></a><br /><br />
<i><span lang="EN-US">The universal proton-motive force</span></i></div>
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<i style="mso-bidi-font-style: normal;"><span lang="EN-US">The
Vital Question</span></i><span lang="EN-US"> offers new glimpses into two of the
most fundamental questions about life: why do all life forms use ion gradients to produce<span style="mso-spacerun: yes;"> </span>energy, and why
eukaryotic cells are the way they are [1]. Now this is quite a programme! And Lane
does a terrific job at presenting us with some of the best past and present
ideas that were put forward in the field (including some of his own). </span></div>
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<span lang="EN-US">Regarding the first question, Lane writes
(p. 65): <i style="mso-bidi-font-style: normal;"> </i></span><br />
<blockquote class="tr_bq">
<span lang="EN-US"><i style="mso-bidi-font-style: normal;">“Life could have been driven by
thermal or mechanical energy, or radioactivity, or electrical discharges, or UV
radiation, the imagination is the limit; but no, all life is driven by redox
chemistry, via remarkably similar respiratory chains.” </i></span></blockquote>
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<tr><td style="text-align: center;"><a href="https://4.bp.blogspot.com/-o_AaRhCrGFo/WVI-a0-1oOI/AAAAAAAAA5g/1ISInU_cNCwh9TBT0pvl6Y_31Jr4S5sCACLcBGAs/s1600/mitchell.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="227" data-original-width="162" src="https://4.bp.blogspot.com/-o_AaRhCrGFo/WVI-a0-1oOI/AAAAAAAAA5g/1ISInU_cNCwh9TBT0pvl6Y_31Jr4S5sCACLcBGAs/s1600/mitchell.jpg" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Peter Mitchell. Source: Nobelprize.org</td></tr>
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<span lang="EN-US">In discussing the vital and universal role
of the proton-motive force in living organisms, which generates ATP (the
energy ‘currency’ in the cell) <span style="mso-spacerun: yes;"> </span>thanks to
a gradient of protons across membranes (see representation of ATP synthase below [<span style="font-size: small;">2])</span>, Lane pays tribute to <a href="http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1978/mitchell-bio.html" target="_blank">Peter Mitchell</a>, the Nobel
laureate who first proposed the concept in the early 1960s, which he then called the
‘chemiosmotic hypothesis’. <span style="mso-spacerun: yes;"> </span>I was
very interested to learn about Mitchell, since as a biology student I was only introduced
to the concept of proton-motive force, not to its history or its discoverer. And as Lane notes
(p. 68), it was once called ‘<i style="mso-bidi-font-style: normal;">the most
counterintuitive idea in biology since Darwin’</i> by the biochemist Leslie
Orgel.</span></div>
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<span lang="EN-US">Lane continues (p. 83):</span></div>
<blockquote class="tr_bq">
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<i style="mso-bidi-font-style: normal;"><span lang="EN-US">“The
evolution of chemiosmotic coupling is a mystery. The fact that all life is
chemiosmotic implies that chemiosmotic coupling arose very early indeed in
evolution.”</span></i></div>
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<tr><td style="text-align: center;"><a href="https://2.bp.blogspot.com/-Sik3B-yEvIs/WVvlx-yC1QI/AAAAAAAAA5w/yYmaKfIdiI02iIEtXmNVTEupW_6Rl6NMwCLcBGAs/s1600/Figure3.9b-reduced.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" data-original-height="1000" data-original-width="875" height="320" src="https://2.bp.blogspot.com/-Sik3B-yEvIs/WVvlx-yC1QI/AAAAAAAAA5w/yYmaKfIdiI02iIEtXmNVTEupW_6Rl6NMwCLcBGAs/s320/Figure3.9b-reduced.jpg" width="280" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The ATP synthase. Image <a href="http://mgl.scripps.edu/people/goodsell/" target="_blank">David Goodsell</a></td></tr>
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<span lang="EN-US">In that context, I<span style="mso-spacerun: yes;"> </span>was amazed to learn that fermentation, which
I thought was some kind of ‘primitive’ way of obtaining energy, is most probably a
more recent invention than the proton-motive force! (p. 168)</span><br />
<br />
<i><span lang="EN-US">The origin of life</span></i></div>
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<span lang="EN-US">Lane delves into hypotheses on the
origin of life with great detail in the second part of the book. It starts with the old ‘primordial soup’ theory that was first proposed by J. B. S. Haldane in 1929 and received support from the famous <a href="https://en.wikipedia.org/wiki/Miller%E2%80%93Urey_experiment" target="_blank">Miller experiment</a> (published in 1953, the same year as Watson
and Crick’s paper on DNA). Miller showed that organic molecules such as amino acids can be formed by the action of lightning on simpler gases like methane, ammonia and hydrogen. Life, the theory posits, would have evolved from those early organic bricks, after they were concentrated by evaporation of tidal pools or by adsorption to inorganic surfaces. As Lane notes, this theory is probably not true, and he explains that the favored explanations now involve deep-sea hydrothermal
vents as primordial life incubators. This theory was prominently developed by <a href="http://www.molevol.hhu.de/en/prof-dr-w-f-martin.html" target="_blank">Bill Martin</a> and <a href="https://science.jpl.nasa.gov/people/Russell/" target="_blank">Mike Russell</a> in the late eighties and in the nineties, and summed up in papers in <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1693102/" target="_blank">2003 </a>and <a href="http://www.nature.com/nrmicro/journal/v6/n11/full/nrmicro1991.html" target="_blank">2008</a>. </span><br />
<br />
<span lang="EN-US">In particular, Martin and Russell have pointed at alkaline deep-sea vents as a possible original cradle for life. In such vents, they argue, exist unique geochemical conditions that could have been the biochemical template for the metabolism of the first living cells. For example, in these vents CO2 is abiotically reduced by H2 into methane (CH4), which is also the reaction that powers autotrophic prokaryotes known as methanogens. In addition, alkaline vents harbor strong pH gradients (i.e., proton gradients) between the alkaline interior and the more neutral seawater, as well as porous structures. And this brings us back to chemiosmotic coupling. Martin <i>et al</i>. note (2008): </span><br />
<blockquote class="tr_bq">
<i><span lang="EN-US">"Accordingly, it has been suggested that the ability to harness a continuous and naturally existing proton gradient at an alkaline hydrothermal vent is older than the ability to generate a proton gradient with a chemistry that is specified by genes. [...] Regarding the question of which came first, there are two simple possibilities: either energy-consuming pumping or energy-conserving chemiosmotic harnessing came first." </span></i></blockquote>
<span lang="EN-US">Martin and Russell favor the latter scenario. The reason why chemiosmotic coupling is universal in living organisms could thus be that early life evolved to use those preexisting proton gradients from deep-sea vents! This, however, is not necessarily how life came to be... But it is an exciting idea that deserves our full attention. As far as I'm concerned, it is still the best hypothesis for the origin of life that I have read. </span><br />
<br />
<span lang="EN-US"><span style="mso-spacerun: yes;">In a follow-up post, I will write about the last part of the book that discusses the origin of complex (eukaryotic) life. <br /> </span></span></div>
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<u>Notes</u></div>
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<span lang="EN-US">[1] Incidently,<span style="mso-spacerun: yes;"> </span>it reminds me of that curious saying: ‘Science
does not answer <i style="mso-bidi-font-style: normal;">why</i> questions, only <i style="mso-bidi-font-style: normal;">how</i> questions’. This is clearly
untrue. Science often deals with ‘why’ questions, in particular questions
pertaining to evolution. I’m not sure why this misleading saying persists, including among scientists…</span><br />
<span lang="EN-US"> [2] Almost all cells use protons, but apparently some anerobic prokaryotic species use sodium ions instead.</span><br />
<span lang="EN-US"><br /></span>
<u><span lang="EN-US">References</span></u><br />
<ul>
<li><span lang="EN-US">Lane, N. (2015) <i><a href="http://nick-lane.net/books/the-vital-question-why-is-life-the-way-it-is/" target="_blank">The Vital Question</a>.</i> Profile Books, London. Paperback edition (2016), 360 p.</span></li>
<li><span lang="EN-US">Martin, W., Baross, J., Kelley, D. and M. J. Russell. (2008) Hydrothermal vents and the origin of life. <i>Nature Reviews Microbiology</i> <b>6</b>: 805-814.</span></li>
</ul>
</div>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com1tag:blogger.com,1999:blog-5916121742642761450.post-64858616336650300802017-03-17T08:57:00.001-07:002017-09-17T10:37:22.133-07:00Cooperation shapes the spatial patterns of bacterial organization<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-bkJFYEJZ27A/WMu-6t1p2uI/AAAAAAAAA3k/zDeAlP-mcPoelIEk201t-Yb8bjz8uZtsQCLcB/s1600/MicroscapesX_crop1.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="205" src="https://1.bp.blogspot.com/-bkJFYEJZ27A/WMu-6t1p2uI/AAAAAAAAA3k/zDeAlP-mcPoelIEk201t-Yb8bjz8uZtsQCLcB/s400/MicroscapesX_crop1.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Cooperative bacterial strains colonizing a surface</td></tr>
</tbody></table>
Bacteria colonize surfaces in all environments. That could be the surfaces of soil aggregates, of rocks in a stream bed, of plant leaves, of animal skin, or that could be the surface of your showerhead... On such surfaces microbes establish complex communities ('biofilms') that can contain many different interacting species. These various species are usually not randomly distributed in the biofilm, but rather organized depending on their environmental preferences (for example some like well-aerated areas, others not so much...) and on the type of interactions that they have with each other. This can result in complex patterns of organization that manifest at the microscopic scale and up to the millimeter scale. Such patterns are not trivial, as they can sustain microbial activity and functions that would not be possible in a well-mixed environment, which has importance for biotechnology applications as well.<br />
<br />
In a new study published this month, we examined the role of cooperation in shaping spatial patterns of bacterial organization on wet surfaces. The paper is available online and is entitled '<a href="http://www.nature.com/articles/srep43726" target="_blank">Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces</a>'. Our idea was that a feeding dependency between two partners would directly control their distribution in space, hence imposing a specific pattern. We used a simple model system made of two bacterial strains that could grow using the chemical compound toluene (a hydrocarbon), but only when they were working together as a 'team' (a bacterial consortium in the jargon).<br />
<a name='more'></a><br />In the illustration below you can see the sequential degradation of toluene by the two bacterial strains (represented with cyan and magenta colors). The photo shows growth on an agar plate with toluene as the sole source of carbon: the strains only form a colony (a few mm wide) when they are spotted together on the agar surface. This way, we force them to cooperate in order to degrade the compound and use it for their cellular growth. If we replace toluene by another compound that both bacteria can use independently, in that case cooperation does not take place - instead, the two bacteria compete for the limited resources available to them.<br />
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://4.bp.blogspot.com/-BOskguUvnzo/WMvQ6mEEI8I/AAAAAAAAA38/xJ0tRDhp_0soMkss0qMCiDSDvoUdOYw5QCLcB/s1600/Figure1_modif.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="226" src="https://4.bp.blogspot.com/-BOskguUvnzo/WMvQ6mEEI8I/AAAAAAAAA38/xJ0tRDhp_0soMkss0qMCiDSDvoUdOYw5QCLcB/s400/Figure1_modif.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><i>Pseudomonas putida </i>(<i>Pp</i>) strains F4 and F107 cooperate to degrade toluene and grow as a colony on a surface</td></tr>
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To visualize the patterns that the bacteria would form, we tagged them with different fluorescent proteins (a green and a red fluorescent protein) that allow us to discriminate them with a fluorescence microscope (see photo below). Using this system, we showed that forced cooperation in toluene degradation results in a form of mutualistic interaction between the strains, that is a 'win-win' situation where both partners benefit. In this scenario, the two bacterial strains tend to self-organize on the surface that they colonize, producing alternate strands distant by only tens of microns. This is dictated by the nature of their interaction: they rely on the diffusion of toluene byproducts from one partner strain to another, therefore they cannot efficiently cooperate if they are too distant from each other. This distinct pattern of organization vanishes when we abolish cooperation and replace it by a competition scenario (in this case, we feed the bacteria with benzoate, a compound that both strains can use independently). By contrast, competition induces a clear segregation between the two bacterial strains, which end up being separated by millimeters in certain areas.<br />
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<tr><td style="text-align: center;"><a href="https://2.bp.blogspot.com/-QzKwUZQHlbg/WMvuk1ZG_JI/AAAAAAAAA4c/ppu6U6umSLsYvmpM7AE_0Ih7lj06Lz9pACLcB/s1600/Consortia4.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="220" src="https://2.bp.blogspot.com/-QzKwUZQHlbg/WMvuk1ZG_JI/AAAAAAAAA4c/ppu6U6umSLsYvmpM7AE_0Ih7lj06Lz9pACLcB/s400/Consortia4.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Patterns of bacterial strains competing or cooperating as they grow on a surface.</td></tr>
</tbody></table>
<br />
The effects of feeding dependency and of diffusion illustrated in this study with a an artificial system also exist in natural habitats. This allows us to make some predictions: for example we would expect to see more spatial organization in environments where steep gradients of one limiting nutrient source are found. Our work is also a step towards a better design of artificial microbial 'landscapes': we need to understand the first principles guiding microbial assembly in order to better control it.<br />
<br />
<br />
<u>References:</u><br />
<ul>
<li>Tecon, R. & Or, D. (2017) <a href="http://www.nature.com/articles/srep43726" target="_blank">Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces</a>. <i>Scientific Reports</i> <b>7</b>, article 43726. </li>
</ul>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com3tag:blogger.com,1999:blog-5916121742642761450.post-16500915698729328882016-09-06T04:49:00.000-07:002017-09-17T10:37:41.744-07:00Symplasmata: a curious case of multicellularity in bacteria<!--[if gte mso 9]><xml>
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<tr><td style="text-align: center;"><a href="https://1.bp.blogspot.com/-XNuYbyXfu3E/V81TVuMqbZI/AAAAAAAAA1A/ywua212OPb0VcPmhdLavS5h2hfhKcLvmQCLcB/s1600/EM7-5-12%2B299R%25234.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="400" src="https://1.bp.blogspot.com/-XNuYbyXfu3E/V81TVuMqbZI/AAAAAAAAA1A/ywua212OPb0VcPmhdLavS5h2hfhKcLvmQCLcB/s400/EM7-5-12%2B299R%25234.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Cells in a symplasmatum and surrounded by a capsule,<br />
seen with transmission electron microscopy.</td></tr>
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<br />
<span lang="EN-US">'<i style="mso-bidi-font-style: normal;">Curiouser
and curiouser’</i>, famously said Lewis Carrol’s Alice, as she was experiencing some very
peculiar events in Wonderland. I have sometimes felt like Alice when I was studying the curious behavior
of the bacterium <i style="mso-bidi-font-style: normal;">Pantoea agglomerans </i><span style="mso-bidi-font-style: normal;">[1], </span></span><span lang="EN-US"><span style="mso-bidi-font-style: normal;"><span lang="EN-US">during my
time in the <a href="http://leveau.ucdavis.edu/">Lab Leveau</a> at UC Davis</span>.</span><sup> </sup></span><br />
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<span lang="EN-US">At first sight, <i style="mso-bidi-font-style: normal;">Pantoea agglomerans</i> looks quite ordinary. It grows as rods a few
micrometers long, it can swim with flagella and it feeds on all sorts of sugars.
It belongs to the family <i style="mso-bidi-font-style: normal;">Enterobacteriaceae</i>,
and thus it is a distant cousin of <i style="mso-bidi-font-style: normal;">E.
coli</i>. You can find <i style="mso-bidi-font-style: normal;">P. agglomerans</i>
in all sorts of environments, but it is particularly good at colonizing the
surface of plants, and in certain cases it competes with pathogens and thus keeps its plant host healthy (that is, it can serve as a biocontrol agent). <a href="https://www.blogger.com/null" name="_GoBack"></a>Because it is a very good leaf colonizer, we have used it in
many studies of bacterial life in the ‘phyllosphere’ (the aerial surfaces of
plants), such as the one described in <a href="http://ofbacteriaandmen.blogspot.ch/2012/03/mechanics-of-bacterial-cluster.html">this previous post</a>. </span></div>
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<span lang="EN-US">Now here’s what special, and actually
seemingly unique, about <i style="mso-bidi-font-style: normal;">Pantoea</i> bacteria.
Under certain conditions, instead of dividing and spreading as individual cells, the bacteria
stay close together and form an aggregate containing up to hundreds of tightly
packed cells. Aggregation is not uncommon in bacteria but, in the case of <i style="mso-bidi-font-style: normal;">Pantoea</i><span style="mso-bidi-font-style: normal;">,</span> cells are constrained by a fibrillar layer, and surrounded by a thick capsule made of polysaccharides,
which indicates some level of cooperation and resources sharing (see image on top of the post). The resulting sausage-shaped structures are called <i style="mso-bidi-font-style: normal;">symplasmata</i> [2]. Interestingly, the species name 'agglomerans'
</span><span lang="EN-US"><span lang="EN-US">(forming
into a ball), which </span>was coined by the great Dutch microbiologist and botanist Martinus Beijerinck in
a paper dating from 1888, probably refers to the species' ability to form symplasmata<span style="font-size: small;"> [3]</span>. Although symplasmata have been known for a very long time, their importance and function in the environment is still a mystery.<span lang="EN-US"> We have observed symplasmata on bean leaf surfaces, and
others have described them attached to the roots of rice plants (<a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.1994.tb00075.x/abstract">Achouak <i>et al.</i>, 1994</a>). What is their ecological role? Does it benefit the plant as well? We do not know yet. </span></span><br />
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<tr><td style="text-align: center;"><a href="https://4.bp.blogspot.com/-wOloQm3rUtQ/V86iiiwGGJI/AAAAAAAAA1o/I_ZH7ACMHOoqkNJKm5iXK_B7Njw4AszlQCLcB/s1600/63X_JBA28_20h_14_shift_crop.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="320" src="https://4.bp.blogspot.com/-wOloQm3rUtQ/V86iiiwGGJI/AAAAAAAAA1o/I_ZH7ACMHOoqkNJKm5iXK_B7Njw4AszlQCLcB/s320/63X_JBA28_20h_14_shift_crop.jpg" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Symplasmata among single cells, seen with light microscopy.<br />
Growing populations always consist of a mix of individual <br />
cells and multicellular symplasmata (we don't know yet why).</td></tr>
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<span lang="EN-US">However, we now better understand how they manage such a feat as making a symplasmatum in the first place, and we just published our findings in the journal <i>Scientific Reports</i>, in a paper entitled '<a href="http://www.nature.com/articles/srep31914">Symplasmata are a clonal, conditional and reversible type of multicellularity</a>'. It took us two breakthrough moments to achieve this. The first one was to find laboratory growth conditions that would allow for symplasmata formation, in order to study them in controlled conditions, without the need of a plant. This was relatively easy: the development of symplasmata is induced in minimal medium with glucose as sole carbon source (if you try to grow them in a rich medium, nothing happens...). Thanks to this convenient way of producing symplasmata in the lab, we found out important facts. First, symplasmata stem from the growth of a single bacterium, hence they are clonal multicellular clusters. Secondly, symplasmata formation is conditional to environmental factors. If you add amino acids, increase the pH or the temperature, no symplasmata are formed. Finally, symplasmata formation is reversible. Under certain conditions cells burst out of their capsule and resume their solitary lifestyle! </span><br />
<br /></div>
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<span lang="EN-US">The second breakthrough involved a much bigger effort. We did a classic genetic study, that is, we looked for mutants of <i>Pantoea agglomerans</i> that were unable to form symplasmata, in order to identify the genes that underlie the clustering phenotype. It would take us forever to find a natural mutant, so we sped up the process using a transposon mutagenesis (we inserted a piece of DNA in the cell that would randomly inactivate a gene on the chromosome). We screened about 5,000 of these mutants, individually, looking at them under the microscope --- fortunately I was not alone to do this!... (Huge thanks to Mila and Irina from Lab Leveau!) This screening allowed us to identify half a dozen protein-coding genes that were directly involved in the formation of symplasmata, including one that helps build the capsule surrounding symplasmata, and one which is a global regulator of gene expression. In addition, we also studied how the whole gene expression profiles changed in symplasmata compared to single cells, and in the wildtype compared to the symplasmata-defficient mutant. Hopefully, this new knowledge will open the way for further studies of symplasmata formation and their ecological role in plant or soil habitats.</span><br />
<span lang="EN-US"><br /></span></div>
<div class="MsoNormal">
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="https://2.bp.blogspot.com/-S-XOSWkWG5o/V86jMcIfAXI/AAAAAAAAA1s/FzZ95rvDGl8mFQPhKQXZdLdmBlvOZDrFgCLcB/s1600/CLSTRS17.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="270" src="https://2.bp.blogspot.com/-S-XOSWkWG5o/V86jMcIfAXI/AAAAAAAAA1s/FzZ95rvDGl8mFQPhKQXZdLdmBlvOZDrFgCLcB/s400/CLSTRS17.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Symplasmata and single cells, seen with scanning electron microscopy. <br />
The capsule was removed by the preparation, but the layer surrounding<br />
the cells appear as an opaque membrane.</td></tr>
</tbody></table>
</div>
<div class="MsoNormal">
<u><span lang="EN-US">Notes</span></u></div>
<div class="MsoNormal">
<span lang="EN-US">[1]. The strain that I have used in the lab,
<i>Pantoea agglomerans</i> 299R, has been reclassified recently as <i style="mso-bidi-font-style: normal;">Pantoea
eucalypti</i> 299R, but I have kept the previous name in this post for historical
reasons.</span></div>
<div class="MsoNormal">
<span lang="EN-US">[2]. Actually, I found out that they were
called that way a long time after I had started studying them... I had even entertained the idea that I was the first one to describe it!... But I couldn't have come out with such a cool name as symplasmata, so all is for the best.</span></div>
<div class="MsoNormal">
<span lang="EN-US">[3]. Since </span><span lang="EN-US"><span lang="EN-US">Beijerinck only mentioned the species in passing in that paper (as '<i>Bacillus agglomerans</i>'),
and without reference to its aggregative behavior, we are left with speculations
regarding the original meaning of ‘agglomerans’. But it seems reasonable to assume the link with symplasmata.</span></span><br />
<br />
<u><span lang="EN-US"><span lang="EN-US">Acknowledgements</span></span></u><br />
<span lang="EN-US"><span lang="EN-US">This research was supported by a VIDI grant to Johan Leveau from the Netherlands Organisation for Scientific Research and by a fellowship to Robin Tecon by the Swiss National Science Foundation.</span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<u><span lang="EN-US"><span lang="EN-US">References</span></span></u></div>
<div class="MsoNormal">
<ul>
<li><span lang="EN-US"><span lang="EN-US">Tecon, R. & Leveau, J. H. J. (2016) <a href="http://www.nature.com/articles/srep31914">Symplasmata are a clonal, conditional and reversible type of multicellularity</a>. <i>Scientific Reports </i>6, article 31914. </span></span></li>
<li><span lang="EN-US"><span lang="EN-US">Achouak, W., Heulin, T., Villemin, G., & Balandreau, J. (1994) <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6941.1994.tb00075.x/abstract">Root colonization by symplasmata-forming <i>Enterobacter agglomerans</i></a>.<i> FEMS Microbiology Ecology </i><b>13</b>, pp. 287-294.<i><br /></i></span></span></li>
</ul>
</div>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com5tag:blogger.com,1999:blog-5916121742642761450.post-6453231660682484852015-04-19T13:01:00.000-07:002015-04-19T13:02:22.129-07:00Principles of Microbial Diversity, by James Brown<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-CTOjiPt_1wM/VTP5cKhvlzI/AAAAAAAAAwg/guXdsJHvOmA/s1600/Brown.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="http://3.bp.blogspot.com/-CTOjiPt_1wM/VTP5cKhvlzI/AAAAAAAAAwg/guXdsJHvOmA/s1600/Brown.jpg" height="320" width="246" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="http://www.asmscience.org/content/book/10.1128/9781555818517">Published by ASM Press</a></td></tr>
</tbody></table>
A new textbook on microbial diversity has just been published by ASM Press. <a href="http://www.asmscience.org/content/book/10.1128/9781555818517"><i>Principles of Microbial Diversity</i></a> is a relatively thin textbook (392 pages) that is intended for undergraduate students who need to follow a course on microbial diversity, hence filling a gap in the available teaching material. His author is <a href="http://www.microbiology.ncsu.edu/people/faculty/Brown.html">James W. Brown</a>, a professor at North Carolina State University. <br />
<br />
The book is pleasant to read and richly illustrated by hundreds of micrographs. But what is quite original, and to me very justified, is the author's perspective, which is, in James Brown's own words in the preface, "<i>phylogenetic and organismal, from the Carl Woese school</i>". I applaud that! Woese, as I discussed in a <a href="http://ofbacteriaandmen.blogspot.ch/2013/01/the-new-biology-of-carl-woese.html">previous post</a>, revolutionized biology by showing that we had until then totally ignored a whole distinct domain of life, the <i>Archaea</i>. This discovery was made through the careful analysis of the sequence of 16S rRNA gene (not an easy feat in the days of Woese's work). Because of this pedagogical and scientifical choice, Brown's book dedicates lots of pages to introduce phylogenetic concepts. Notably, he gives a didactic and useful explanation of how to construct a phylogenetic tree (Chapter 3). Brown explains his focus as follows (p. 351):<br />
<blockquote class="tr_bq">
<i>"In this book, the vantage point from which all of microbial diversity is viewed is the phylogenetic perspective. Other perspectives are possible and are very useful. Medical microbiology views the microbial world from the perspective of its influence on microbe-human interactions and human health. Environmental microbiology views the microbial world from the perspective of biogeochemical processes and ecosystems. <span lang="EN-US">[…] However, the organizing principle of biology is evolutionary theory. The phylogenetic perspective is the view of biological diversity as the outcome of evolutionary history. This perspective is not exclusive of any other perspective on microbiology, but instead enriches these other perspectives."</span></i></blockquote>
Brown's textbook contribution is very welcome, and should find a place in each university's library.<br />
<br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/--7stM3N1X3E/VTQHNOAyHoI/AAAAAAAAAww/nmk1jaG1wIU/s1600/Arcella_sp.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://1.bp.blogspot.com/--7stM3N1X3E/VTQHNOAyHoI/AAAAAAAAAww/nmk1jaG1wIU/s1600/Arcella_sp.jpg" height="400" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Example of book photo. The eukaryote <i>Arcella</i>. Source: <a href="http://commons.wikimedia.org/wiki/File:Arcella_sp.jpg">Wikimedia Commons</a></td></tr>
</tbody></table>
<br />
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<u>References:</u><br />
<ul>
<li>Brown, J. W. (2015) <a href="http://www.asmscience.org/content/book/10.1128/9781555818517">Principles of Microbial Diversity</a>. ASM Press, Washington DC. 392 pages.</li>
</ul>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com0tag:blogger.com,1999:blog-5916121742642761450.post-34483414865078754202015-02-24T11:44:00.002-08:002015-04-19T13:01:45.072-07:00Mining soil for new antibiotics<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-AowZmoaP0nY/VOzSNqEgI_I/AAAAAAAAAvk/gvaP52RbFQw/s1600/MRSA.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="http://2.bp.blogspot.com/-AowZmoaP0nY/VOzSNqEgI_I/AAAAAAAAAvk/gvaP52RbFQw/s1600/MRSA.jpg" height="320" width="242" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Methicillin-resistant <i>Staph aureus</i>. <a href="https://www.flickr.com/photos/niaid/8423852305/in/photostream/">Photo NIAID</a></td></tr>
</tbody></table>
The beginning of 2015 brought (potentially) good news for medicine: the discovery of a new antibiotic - teixobactin - isolated from soil bacteria. <a href="http://www.nature.com/nature/journal/v517/n7535/full/nature14098.html">This result was published in <i>Nature </i>on January 22</a>. (Unfortunately the whole text is not visible without payment or subscription.) Many newspapers and news outlets covered the story in early January, for instance <a href="http://www.theguardian.com/science/2015/jan/07/antibiotic-drug-resistance-teixobactin"><i>the Guardian</i></a>, and the <a href="http://www.nytimes.com/2015/01/08/health/from-a-pile-of-dirt-hope-for-a-powerful-new-antibiotic.html?_r=1"><i>New York Times</i></a>. Teixobactin is a small peptide that acts as an inhibitor of cell wall synthesis in Gram-positive bacteria, which means it can kill pathogens like drug-resistant <i>Staphylococcus aureus </i>(often referred to as MRSA, or methicillin-resistant <i>S. aureus</i>).<br />
<br />
The issue at stake here is, of course, the increasing prevalence of antibiotic-resistant bacteria worldwide, a situation well summarized in <a href="http://www.swissinfo.ch/eng/medicine-has-lost-ground-in-race-against-germs/41277274">an article at Swissinfo.ch</a>. We have thus seen a dramatic increase in resistant strains of, for instance, <i>S. aureus</i>, <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i>. Who or what is to blame? Most probably the overuse of antibiotics, not only in humans but also in animals. It is frightening to know that some pathogenic strains can survive our entire arsenal of antibiotics, while new potent drugs are extremely hard to find. Some simple solutions have helped mitigate the problem, notably more effective and systematic hand disinfection by hopital personnel, but this will not prevent all cases of infection. New antimicrobials are clearly needed, but where to find them?<br />
<br />
<a name='more'></a><br /><br />
Historically, soil bacteria have been our major source of antimicrobial compounds, particularly the genus <a href="https://microbewiki.kenyon.edu/index.php/Streptomyces"><i>Streptomyces</i></a>. The discovery of new antibiotics from soil bacteria, however, has stalled in the past decades. One obvious reason is that we have already collected the low-hanging fruits: that is, compounds that are easy to isolate from bacteria that easily grow in the laboratory. The pool of remaining antimicrobial compounds in nature might be enormous, but the effort to mine it is substantial. This is what makes the paper by Ling and colleagues so interesting: it shows that we can extract useful drugs from soil microorganisms that are not readily cultivable in the laboratory. <br />
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-j1RB2IfqQ28/VOzTABoT8II/AAAAAAAAAvs/OzF0NYPvyRU/s1600/Teixobactin.svg.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="http://3.bp.blogspot.com/-j1RB2IfqQ28/VOzTABoT8II/AAAAAAAAAvs/OzF0NYPvyRU/s1600/Teixobactin.svg.png" height="220" width="320" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Structure of Teixobactin. Source <a href="http://commons.wikimedia.org/wiki/Category:Teixobactin#mediaviewer/File:Teixobactin.svg">Wikimedia commons</a>.</td></tr>
</tbody></table>
This feat was achieved by an international team of researchers from <a href="http://www.northeastern.edu/">Northeastern University</a> in Boston, the <a href="http://www3.uni-bonn.de/">University of Bonn</a>, and the biotech company <a href="http://www.novobiotic.com/">NovoBiotic Pharmaceuticals</a>. To isolate the soil bacteria, they used a clever device named the iChip (<a href="http://www.ncbi.nlm.nih.gov/pubmed/20173072">Nichols et al., 2010</a>, and see also this interesting post at <a href="http://www.popsci.com/ichip-new-way-find-antibiotics-and-other-key-drugs"><i>Popular Science</i></a>). This chip, designed by <a href="http://www.northeastern.edu/epsteinlab/">the group of Slava Epstein</a>, consists of 192 microwells isolated between two permeable membranes. Once trapped in a microwell, the bacteria can be cultivated directly in soil (where the bacteria can be in contact with soil nutrients, but cannot escape), as opposed to classic plating techniques on Petri dishes. The screening of ~10,000 individual soil isolates permitted the discovery of a new species - named <i>Eleftheria terrae</i>, and belonging to beta-Proteobacteria -, which produces teixobactin. Needless to say, the iChip could lead to the discovery of many other uncultivable species producing compounds of medical importance. This is a great example of how the quest for new drugs is taking place in natural environments rather than in chemical synthesis lab (see for instance my <a href="http://ofbacteriaandmen.blogspot.ch/2014/02/oceans-bacteria-and-quest-for-new-drugs.html">previous post</a> on mining the deep sea for active compounds).<br />
<br />
One downside is that teixobactin is only active against Gram-positive bacteria (<i>Staphylococcus</i>, <i>Bacillus</i>, <i>Clostridium, Mycobacterium</i>, etc.), whereas the most pressing problems are related to Gram-negative species. This notwithstanding, the discovery of teixobactin is a step in the right direction.<br />
<br />
<u>References:</u><br />
<ul>
<li>Ling, L. L., <i>et al.</i> (2015) <a href="http://www.nature.com/nature/journal/v517/n7535/full/nature14098.html">A new antibiotic kills pathogens without detectable resistance.</a> <i>Nature </i>517: pp.455-459.</li>
<li>Nichols, D., <i>et al.</i> (2010) <a href="http://www.ncbi.nlm.nih.gov/pubmed/20173072">Use of iChip for high-throughput in situ cultivation of "uncultivable" microbial species</a>. <i>Applied Environmental Microbiology</i> 76(8): pp. 2445-2450.</li>
</ul>
<h1>
</h1>
<br />
<br />
<br />
<br />Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com1tag:blogger.com,1999:blog-5916121742642761450.post-77565553229430138202015-01-26T12:12:00.001-08:002015-02-24T11:50:32.443-08:00The Logic of Life, by François Jacob<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-pNjC4gdZbZc/VMaeagSC1CI/AAAAAAAAAvE/QC13K1JLHIo/s1600/LdV.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="http://2.bp.blogspot.com/-pNjC4gdZbZc/VMaeagSC1CI/AAAAAAAAAvE/QC13K1JLHIo/s1600/LdV.jpg" height="320" width="210" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><br /></td></tr>
</tbody></table>
<i>The Logic of Life</i> (<a href="http://www.gallimard.fr/Catalogue/GALLIMARD/Tel/La-Logique-du-vivant"><i>La logique du vivant</i></a>) opens with the following quote by the French philosopher and Enlightenment figure Denis Diderot:<br />
<blockquote class="tr_bq">
<i>"Do you see this egg? It's with it that we overturn all theological schools and all temples on Earth".</i> </blockquote>
<blockquote class="tr_bq">
[All translations in this post are mine.]</blockquote>
The choice of a 18th century thinker for the epigraph prefigures a lot of this book, which was published by the late Nobel laureate <a href="http://ofbacteriaandmen.blogspot.ch/2013/05/adieu-francois-jacob.html">François Jacob</a> in 1970. The book<!--[if gte mso 9]><xml>
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</xml><![endif]--><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: DE-CH; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">—</span>thus proves to be of great erudition and cites the original work of, among many names, Paré, Montaigne, Paracelse, Descartes, Galilée, Harvey, Réaumur, Buffon, Redi, Leibniz, D'Holbach, La Mettrie, Lamarck, Linné, Geoffroy Saint-Hilaire... and I haven't even mentioned the 20th century references yet! Excusez du peu!<br />
<br />
This story of heredity truly is a huge endeavor, spanning about four centuries of philosophical and scientific attempts to understand what kind of stuff we're made of. Articulated in long chapters that correspond to conceptual milestones ("visible structure", "organization", "time", "gene", "molecule", and "integron"), the book follows the chronological development of our biological knowledge (which was part of "natural philosophy") with plenty of referenced sources and with a quality of writing that is hardly matched today. <br />
<br />
<a name='more'></a><br /><br />
This "history of heredity" reads also somewhat as a history of biology. Our understanding of living things ("le vivant"), interestingly, evolved through extreme stages, as Jacob explains throughout the book: from being of the same essence than the inert world (17th century and before), to being something different altogether<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: DE-CH; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">, possessing a vital force (18th)—</span>and back to being not fundamentally different from the rest of the physical world (19th century to this day).<br />
<br />
One thing I particularly enjoy about <i>the logic of life </i>is how it shows us the genius of minds from the past, as they show extraordinary insights given the limits of their time. For instance (translations are mine):<br />
<br />
<a href="http://en.wikipedia.org/wiki/%C3%89tienne_Geoffroy_Saint-Hilaire">Geoffroy Saint-Hilaire</a>:<br />
<blockquote class="tr_bq">
<i>"Nature constantly uses the same materials and is ingenious only in varying its forms."</i></blockquote>
<a href="http://en.wikipedia.org/wiki/Georges_Cuvier">Cuvier</a>, talking about an organism and how it interacts with its environment:<br />
<blockquote class="tr_bq">
<i>"Its sphere spreads beyond the limits of the living body itself."</i></blockquote>
<a href="http://en.wikipedia.org/wiki/Antoine_Lavoisier">Lavoisier</a>:<br />
<blockquote class="tr_bq">
<i>"The animal machine is governed by three principal regulators: respiration, which consumes oxygen and carbon and produces calorific; transpiration, which increases or decreases depending on calorific needs; finally digestion, which gives back to blood what it loses by respiration and transpiration."</i></blockquote>
Jacob is undoubtedly one of these great minds (he helped create molecular biology!). Interestingly, Jacob shows us in his book how the development of biology is tightly intertwined with the development of the other sciences, notably physics and chemistry. He insists, for instance, on the parallels between population biology (starting with Darwin) and statistical mechanics (with Gibbs and Boltzmann): both are laws that consider very large numbers (of organisms or atoms). He writes (p. 213):<i> "The concepts of energy and equivalence thus come play one of the roles that biology in its youth had to give to vital force."</i><br />
And this analysis, p. 266:<br />
<blockquote class="tr_bq">
<i>"To constitute itself as a science, biology had to distantiate itself radically from physics and chemistry. In the middle of the twentieth century, to continue the analysis of the structure of living beings and their functioning, it has to closely associate with them. From this union will come molecular biology." </i></blockquote>
This is a clever and important book, highly recommended!<br />
<br />
<u>References:</u><br />
<ul>
<li>Jacob, François. (1970) <a href="http://www.gallimard.fr/Catalogue/GALLIMARD/Tel/La-Logique-du-vivant"><i>La logique du vivant</i></a>. Collection Tel, Gallimard. 352 pages.</li>
<li>English translation: Jacob, François. (1993) <i><a href="http://press.princeton.edu/titles/5200.html">The Logic of Life: A history of heredity</a>. </i>(Translated by Betty Spillmann.) Princeton University Press. 368 pages.</li>
</ul>
<br />Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com1tag:blogger.com,1999:blog-5916121742642761450.post-64382431356961574242014-08-31T04:51:00.000-07:002015-02-15T00:15:03.652-08:00The debate over influenza research is still on<!--[if gte mso 9]><xml>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-3dpgb0e--8M/VAL3HzJdGCI/AAAAAAAAAsA/-lGJ37fsJ2I/s1600/H5N1_virion.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="http://1.bp.blogspot.com/-3dpgb0e--8M/VAL3HzJdGCI/AAAAAAAAAsA/-lGJ37fsJ2I/s1600/H5N1_virion.jpg" height="320" width="269" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">H5N1 virion. Photo <a href="http://commons.wikimedia.org/wiki/H5N1#mediaviewer/File:A_%28H5N1%29_virion,_a_type_of_bird_flu_virus_which_is_a_subtype_of_avian_influenza_A.jpg">Cynthia Goldsmith/Jackie Katz</a></td></tr>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">Two years
ago, a controversy emerged about the research on influenza virus H5N1, and the
potential risk associated with it. This controversy followed the publication of
two research articles in <i style="mso-bidi-font-style: normal;">Science</i> and <i style="mso-bidi-font-style: normal;">Nature</i>, and I wrote about it in January
2012 <a href="http://ofbacteriaandmen.blogspot.ch/2012/01/controversy-over-h5n1-research.html">in this blog post</a>. Briefly, scientists have used so-called “gain-of-functions”
experiments, in which strains of influenza viruses are selected for new traits
such as higher transmissibility between ferrets (the preferred animal model in these studies). The objections that were raised by some critics
of this research were of two kinds: first, the information available in these
papers could be used by terrorists in order to produce bioweapons; second,
modified influenza viruses could escape the lab by accident and create a
pandemic. The first objection led to a very rare decision in scientific
publishing, namely the redaction of the articles to remove potentially
sensitive data. The important public concern also led the authors of these
studies to promulgate a moratorium on this type of work. After this temporary
stop, the experiments started again with additional biosafety measures. </span></div>
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<br /></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">The debate,
however, is far from over. The reason for this? Well, the recent publications
of several studies dealing with influenza virus, most notably <a href="http://www.cell.com/cell-host-microbe/abstract/S1931-3128%2814%2900163-2">a paper</a> by Y.
Kawaoka (the author of the 2012 <i>Nature </i>publication) on avian influenza viruses
related to the 1918 “Spanish flu” virus. This research triggered a heated
response from several scientists, which was loudly echoed in the mainstream
press (see for instance in the <a href="http://www.theguardian.com/science/2014/jun/11/crazy-dangerous-creation-deadly-airborne-flu-virus">Guardian </a>and in the <a href="http://www.independent.co.uk/news/science/exclusive-controversial-us-scientist-creates-deadly-new-flu-strain-for-pandemic-research-9577088.html">Independent</a>). In that
particular case, it seems that the scientific community is truly divided on
the matter. An example of this dissent was the publication of a statement of
concern by a group of scientists known as the <a href="http://www.cambridgeworkinggroup.org/">Cambridge Working Group</a>,
which in essence asked for a better assessment of the risks of virus
research via the organization of a conference that would deal with all present
issues. Such a meeting could resemble the famous <a href="http://en.wikipedia.org/wiki/Asilomar_Conference_on_Recombinant_DNA">Asilomar </a>conference of 1975,
where the risks associated with recombinant DNA were debated. Other
virologists, however, have fought back these reactions of distrust and have
created another group, <a href="http://www.scientistsforscience.org/">Scientists for Science</a>, which aims at promoting the
benefits of this research, and highlight the fact that serious safety regulations are already in place for virus research. </span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">The
situation, it seems to me, is now polarized between a pro and an anti camp. In
the 'anti' camp, we find for instance <a href="http://www.hsph.harvard.edu/marc-lipsitch/">Marc Lipsitch</a>, an
epidemiologist from Harvard who published <a href="http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1001646#pmed-1001646-t002">a paper</a> criticizing this research, and <a href="http://gasp.med.harvard.edu/members/rkolter.html">Roberto Kolter</a>, microbiologist and former president of the American Society for Microbiology, also from Harvard, who was quoted <a href="http://www.independent.co.uk/news/science/american-scientists-controversially-recreate-deadly-spanish-flu-virus-9529707.html">in the Independent</a> saying that </span>“<i>the scientists doing this work are so immersed in their own
self-aggrandisement, they have become completely blind to the
irresponsibility of their acts</i>".<span lang="EN-US" style="mso-ansi-language: EN-US;"> Defending
the validity of the research on influenza virus we find, of course, Kawaoka himself, who insists that the knowledge we gain on viruses can help save lives.
Other open and vocal supporters of the research include <a href="http://www.microbiology.columbia.edu/faculty/racaniello.html">Vincent Racaniello</a>, virologist
at Columbia University and host of the excellent <a href="http://www.microbeworld.org/podcasts/this-week-in-microbiology">TWiM</a> and <a href="http://www.twiv.tv/">TWiV</a> podcasts, <a href="http://www.virology.ws/2014/07/04/the-value-of-influenza-aerosol-transmission-experiments/">who defends the value of these experiments</a>. Racaniello denounces the misrepresentation of the nature of these modified viruses, and the exaggerated claim that they could be deadlier than previous pandemic viruses. His “Ferrets are
not humans!” has become almost a leitmotiv: he means by this that <a href="http://www.virology.ws/2011/12/06/ferreting-out-influenza-h5n1/">transmissibility between ferrets does not entail transmissibility between humans</a>. </span>
</div>
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<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Fortunately,
the divide between the two camps is not at all irreconcilable. Both camps are
in favor of the convening of an Asilomar-type conference, and this could be the
opportunity to assess the situation with an open mind and the best of our
current science. This, at least, is advocated by Arturo Casadevall and Michael
Imperiale in <a href="http://mbio.asm.org/content/5/4/e01730-14.short">a very recent paper</a> in <i>mBio</i>. (This excellent paper was an
inspiration for this blog post, and many of my summary elements come from it;
it is a must-read for anyone who wants to get the full picture of the debate at
play.) Casadevall and Imperiale rightly point out that the value of
gain-of-functions experiments is not contested, but they “<i>believe that the crux of the
debate surrounding GOF experiments is not their value but their potential risk</i>”
(p.2). </span></div>
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<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Indeed, one
thing that muddles the debate is the difficulty to estimate the risk-benefit of
such experiments. Recent <a href="http://www.theguardian.com/science/2014/jul/11/two-us-government-labs-shut-down-troubling-safety-lapses">biosafety failures</a> in prestigious institutions such as
the <a href="http://www.cdc.gov/">Center for Disease Control</a> in Atlanta have shown that accidents can
happen. In that respect, I believe it is disingenuous to affirm that
lab-modified viruses could not escape. The key thing, here, is the dangerosity
of these lab strains. It seems clear that the media and some scientists were
guilty of using an exaggerated rhetoric, talking about 'doomsday' and the 'deadliest' virus (read <a href="http://www.virology.ws/2013/02/18/harvard-university-great-virology-bad-science-writing/">Racaniello's take on this rhetoric</a>). On the other hand, the unintentional
release of a lab virus, and the consequences of it, could be disastrous for
the population and for science as a whole. I cannot help feeling worried at the thought of recombined
viruses escaping the lab. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Hopefully,
this global conference will be organized soon, and decisions will be taken that
advance both research and public safety. That would be much needed.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<u><span lang="EN-US" style="mso-ansi-language: EN-US;">References:</span></u></div>
<br />
<ul>
<li><span lang="EN-US" style="mso-ansi-language: EN-US;">Casadevall
A. and M. Imperiale (2014). <a href="http://mbio.asm.org/content/5/4/e01730-14.short">Risks and benefits of gain-of-function experimentswith pathogens of pandemic potential, such as influenza virus: a call for ascience-based discussion</a><b>.</b> <i>mBio </i>5:4.</span></li>
<li><span lang="EN-US" style="mso-ansi-language: EN-US;">Lipsitch M.
and A. P. Galvani (2014). <a href="http://www.plosmedicine.org/article/info%3Adoi%2F10.1371%2Fjournal.pmed.1001646#pmed-1001646-t002">Ethical alternatives to experiments with novelpotential pandemic pathogens</a>. <i>PLoS Medicine</i>. 11:5. </span></li>
<li><span lang="EN-US" style="mso-ansi-language: EN-US;">Watanabe T.
<i>et al.</i> (2014). <a href="http://www.cell.com/cell-host-microbe/abstract/S1931-3128%2814%2900163-2">Circulating avian influenza viruses closely related to the 1918virus have pandemic potential</a>. <i>Cell Host & Microbe</i> <b>15</b>: pp.692-705 </span></li>
</ul>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com3tag:blogger.com,1999:blog-5916121742642761450.post-21299139569031819832014-08-03T07:45:00.000-07:002014-08-31T04:53:46.396-07:00Microbe Hunters by Paul de Kruif<!--[if gte mso 9]><xml>
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<div class="separator" style="clear: both; text-align: center;">
<a href="http://3.bp.blogspot.com/-43jFSrm0Jcc/U95JMno8SdI/AAAAAAAAArU/ORKoQJG3VL0/s1600/milstein-early-l2.jpg" imageanchor="1" style="clear: left; float: left; margin-bottom: 1em; margin-right: 1em;"><img border="0" src="http://3.bp.blogspot.com/-43jFSrm0Jcc/U95JMno8SdI/AAAAAAAAArU/ORKoQJG3VL0/s1600/milstein-early-l2.jpg" height="320" width="200" /></a></div>
<div class="MsoNormal">
<span style="mso-ansi-language: EN-US;"><span style="mso-spacerun: yes;"></span><span lang="EN-US">‘<i style="mso-bidi-font-style: normal;">Microbe Hunters’</i>, as I have often been told, is a classic reading
in microbiology—one of those books that can inspire the beginning of a career.
In this book, written in 1926, American microbiologist and author <a href="http://en.wikipedia.org/wiki/Paul_de_Kruif">Paul de Kruif</a> proposes to acquaint us with the great pioneers of microbiology, from Leeuwenhoek
to Ehrlich, via Pasteur, Koch, Roux and several more. </span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">I gave it a
try, and I must confess that at first I was a bit taken aback by the quite
unusual style of the author: extremely enthusiastic, overly lyric, made to
immerge us in the life of the protagonists with a plethora of details that may
or may not be true.<span style="mso-spacerun: yes;"> </span>I can’t remember
reading anything quite approaching the surprising and unusual tone of <i style="mso-bidi-font-style: normal;">Microbe Hunters</i>. Here’s an example describing
Spallanzani’s early experiments (p. 34):</span></div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
<i><span lang="EN-US" style="mso-ansi-language: EN-US;">“What’s
this?” [Spallanzani] cried. Here and there in the gray field of his lens he
made out an animalcule playing and sporting about—these weren’t large microbes,
like some he had seen—but they were living little animals just the same.</span></i></div>
<div class="MsoNormal">
<i><span lang="EN-US" style="mso-ansi-language: EN-US;">“Why, they
look like little fishes, tiny as ants,” he muttered—and then something dawned
on him— “These flasks were sealed- nothing could get into them from the
outside, yet here are little beings that have stood a heat of boiling water for
several minutes!” </span></i></div>
<div class="MsoNormal">
<i><span lang="EN-US" style="mso-ansi-language: EN-US;">[…] It was
a great day for Spallanzani, and though he did not know it, a great day for the
world. </span></i></div>
</blockquote>
<br />
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">But as I
was reading further I grew accustomed to this prose, and, to my own surprise, I
started to enjoy it! It is indeed difficult not to share de Kruif’s enthusiasm
for these great men of the past and, even though I would take the author’s
factual accuracy with more than a grain of salt, the book really makes you want
to learn more about the personal life of these pioneers.</span></div>
<div class="MsoNormal">
<br />
<a name='more'></a><br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Notably,
the figures of Pasteur and Koch are vividly brought to us, and the comparison
of the two is striking (p.147-148):</span></div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
<i><span lang="EN-US" style="mso-ansi-language: EN-US;">Nothing is
truer than that there is no one orthodox way of hunting microbes, and the
differences between the ways Koch and Pasteur went at their work are the best
illustrations of this. Koch was as coldly logical as a text-book of geometry—he
searched out his bacillus of tuberculosis with systematic experiments, and he
thought of all the objections that doubters might make before such doubters
knew that there was anything to have doubts about. Koch always recited his
failures with just as much and no more enthusiasm than he did his triumphs.
There was something inhumanly just and right about him and he looked at his own
discoveries as if they had been those of another man of whom he was a little
over-critical. But Pasteur! This man was a passionate groper whose head was
incessantly inventing right theories and wrong guesses—shooting them out like a
display of village fireworks going off bewilderingly by accident.</span></i></div>
</blockquote>
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-eSlyl6aBYjo/U95JlMdwIOI/AAAAAAAAArc/duc5nQ47yFg/s1600/Louis_Pasteur_from_Galerie_Contemporaine.jpg" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="http://3.bp.blogspot.com/-eSlyl6aBYjo/U95JlMdwIOI/AAAAAAAAArc/duc5nQ47yFg/s1600/Louis_Pasteur_from_Galerie_Contemporaine.jpg" height="400" width="318" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">The great Pasteur, one of the "microbe hunters"(<a href="http://commons.wikimedia.org/wiki/Louis_Pasteur#mediaviewer/File:Louis_Pasteur_from_Galerie_Contemporaine.jpg">Wikimedia Commons</a>)</td></tr>
</tbody></table>
<br />
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">De Kruif
does a great job at describing the great endeavors accomplished by these men,
who were motivated both by scientific curiosity and by societal necessity: in
the 19<sup>th</sup> century, the toll paid by the human race to contagious
diseases was enormous. Because, in important aspects, the story of
microbiologists is the story of hunting diseases: anthrax, transmitted by the spores
of the bacterium <i style="mso-bidi-font-style: normal;">Bacillus anthracis</i> (Koch
identified the germ, and Pasteur developed the first vaccine in 1881); rabies,
the viral disease also fought by Pasteur; diphtheria, caused by a bacterial
toxin; Texas fever, due to a Protozoan that infects cattle via a tick; the
sleeping sickness, a <i style="mso-bidi-font-style: normal;">Trypanosoma</i>
transmitted to humans via the tsetse fly; and malaria, of course, caused by
another Protozoan transmitted by a mosquito. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">De Kruif is
optimistic (and enthusiastic!) about the power of men of science to fight
infectious diseases and thus alleviate the sufferings of mankind. It is worth
noting that <i style="mso-bidi-font-style: normal;">Microbe Hunters</i> was
published two years <i style="mso-bidi-font-style: normal;">before</i> what would
become the greatest discovery of all times: the discovery of penicillin by
Fleming. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">I would recommend Microbe Hunters, as long as one accepts its exuberance (or maybe because of it!).</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<u><span lang="EN-US" style="mso-ansi-language: EN-US;">Reference:</span></u></div>
<br />
<ul>
<li><span lang="EN-US" style="mso-ansi-language: EN-US;">De Kruif, Paul. (1926) <i>Microbe Hunters</i>. Blue Ribbon Books, New York. 365 pages.</span></li>
</ul>
<span lang="EN-US" style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-font-size: 10.0pt; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: DE-CH; mso-fareast-theme-font: minor-fareast; mso-hansi-theme-font: minor-latin;"></span>Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com3tag:blogger.com,1999:blog-5916121742642761450.post-9840393795036813342014-02-23T13:17:00.003-08:002014-08-31T05:00:05.667-07:00Oceans, bacteria, and the quest for new drugs<!--[if gte mso 9]><xml>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-qyPsXpFCEjI/Uwn15b-bhEI/AAAAAAAAApk/ZBtoaEo-c_Y/s1600/800px-Theonella_cylindrica_%2528Tube_sponge%2529.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://4.bp.blogspot.com/-qyPsXpFCEjI/Uwn15b-bhEI/AAAAAAAAApk/ZBtoaEo-c_Y/s1600/800px-Theonella_cylindrica_%2528Tube_sponge%2529.jpg" height="300" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">A<i> </i>marine sponge of the genus <i>Theonella</i>. <a href="http://commons.wikimedia.org/wiki/File:Theonella_cylindrica_%28Tube_sponge%29.jpg">Photo by Nick Hobgood</a>.</td></tr>
</tbody></table>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;"><span id="goog_1155874208"></span><span id="goog_1155874209"></span>We rely on
natural products in medicine: the vast majority of pharmaceutical drugs are
thus of plant or microbial origin. (The purely synthetic drugs, which have no
counterparts in the environment, are the exception rather than the rule.) To
name potent examples of natural products, take antibiotics (discovered in fungi
and bacteria), the anti-malaria drug artemisinin (isolated from sweet wormwood)
or simply aspirin (salicylic acid is present in willow bark). Many people, I
think, forget about this, as they oppose a so-called ‘natural’ medicine to a ‘chemical’
medicine (the pills you get from your doctor). </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">It is not
easy to find new active compounds, however, and much more difficult to test
them and turn them into a real medicine. The situation doesn’t look that good,
notably because of the high increase of antibiotic-resistant strains of
bacteria, and the paucity of new drugs available. A natural environment that
has long been recognized as a promising source of new chemicals is the largest
on Earth—oceans—, and many researchers are mining the sea in search of new
organisms and their specific biochemical abilities. For instance, the research
project <a href="http://www.pharma-sea.eu/">PharmaSea</a>, funded by the European Union, was launched in 2013 with the
goal of discovering new microbial organisms that could be the source of useful chemicals
for medicine or industry. This team of academics and industry researchers plan
to explore the deep bottom of the sea, looking for environments that are poorly
known and potentially harbor interesting organisms. Here’s an excerpt from the project
website:</span></div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">“</span></i><span style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Marine organisms that live more than 6,000
meters below the sea level are considered to be an interesting source of novel
bioactive compounds as they survive under extreme conditions.</span></span><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;"> "Trenches
are separated from each other and represent islands of diversity. They are not
connected to each other and life has evolved differently in each one",
</span></i><span style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">explains Marcel Jaspars</span></span><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;"> </span></i><span style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">[PharmaSea project leader]</span></span><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">. “</span></i></div>
</blockquote>
<br />
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">PharmaSea is an
ambitious project, and it may not be easy at all to get many new products out
of it, but the goal has to be praised, as we surely are in need of new
biochemicals, particularly new antibiotics.</span></div>
<div class="MsoNormal">
<br />
<a name='more'></a><br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Another
exciting example of ocean biodiscovery was recently published in the journal <i style="mso-bidi-font-style: normal;">Nature</i>. It is the collaboration of research
groups in Japan, Germany, USA and Switzerland, and led by <a href="http://www.micro.biol.ethz.ch/research/piel/jpiel">Jörn Piel</a>,
professor in the Institute of Microbiology at ETH Zürich. (A summary of the
findings was published on the <a href="https://www.ethz.ch/en/news-and-events/eth-news/news/2014/01/sponge-bacteria.html">ETH News website</a>.) This team of scientists is
interested in a species of marine sponge, <i style="mso-bidi-font-style: normal;">Theonella
swinhoei</i>, which is known to produce many bioactive compounds (notably
polytheonamides). The sponge, however, is not producing these chemicals itself;
instead, symbiotic microorganisms are doing the job. It’s worth knowing that
most sponge species live in close association with a large consortium of many
diverse bacteria (not unlike the bacterial flora in our gut), and that most of
these bacteria are unknown to us and can’t even be grown in the laboratory. </span></div>
<div class="MsoNormal">
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-2RirAvYokpg/Uwpj8B5xWTI/AAAAAAAAAp8/0vk093nu_S0/s1600/Theonellamide_F.svg.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://4.bp.blogspot.com/-2RirAvYokpg/Uwpj8B5xWTI/AAAAAAAAAp8/0vk093nu_S0/s1600/Theonellamide_F.svg.png" height="183" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Example of a bioactive compound from <i>Theonella</i>: <a href="http://commons.wikimedia.org/wiki/File:Theonellamide_F.svg">Theonellamide F,</a> a fungicide.</td></tr>
</tbody></table>
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
</div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">The
group of Prof. Piel identified a new group of bacteria, living in symbiosis
with <i style="mso-bidi-font-style: normal;">Theonella swinhoei</i>, which is
responsible for the synthesis of most bioactive compounds in the sponge; they proposed
a new genus name (<i style="mso-bidi-font-style: normal;">Entotheonella</i>) and
even a new taxon (Tectomicrobia) to characterize these microorganisms. Many advanced
techniques were necessary for this breakthrough, including single-cell genome
analysis. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">The
discovery of a new potent drug producer, as exciting as it is, is far from the
end of the story. One major issue is to extract enough material to pursue
clinical trials, something not easy with marine sponges, which at present
cannot be cultivated. What is more, most of these compounds are too complex to
be synthesized chemically. But if we could harness the biochemical ability of
the sponge microorganisms, <i style="mso-bidi-font-style: normal;">outside of
their host</i>, this would offer an alternative. That, unfortunately, is not
guaranteed to work, as microorganisms grown in pure cultures in the lab often
behave unpredictably (in that case, that could be by stopping
the production of bioactive compounds). A third route exists: using bioengineering
technology to transfer <i style="mso-bidi-font-style: normal;">Entotheonella</i>’s
ability to produce bioactive compounds in other, more amenable microorganisms
(say, yeast or <i style="mso-bidi-font-style: normal;">E. coli</i>). In other
words, it’s still a long way to the development of useful drugs from sponge
microbes. But, at least, there is a way.</span></div>
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<br /></div>
<div class="MsoNormal">
<u><span lang="EN-US" style="mso-ansi-language: EN-US;">References:</span></u></div>
<br />
<ul>
<li><span lang="FR-CH" style="mso-ansi-language: FR-CH;">Wilson M.
C., <i style="mso-bidi-font-style: normal;">et al.</i> (2014). </span><span lang="EN-US" style="mso-ansi-language: EN-US;"><a href="http://www.nature.com/nature/journal/v506/n7486/full/nature12959.html">An environmental bacterial taxon with a large and distinct metabolic repertoire</a>. <i style="mso-bidi-font-style: normal;">Nature</i> 506: pp. 58-61. <span style="mso-spacerun: yes;"> </span></span>doi:10.1038/nature12959</li>
</ul>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com3tag:blogger.com,1999:blog-5916121742642761450.post-60746407752178958592014-01-26T03:04:00.000-08:002014-02-23T13:23:32.574-08:00Communicating science: TED talks<!--[if gte mso 9]><xml>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">Is it even necessary
to introduce <a href="http://www.ted.com/">TED </a>talks?... <span style="mso-spacerun: yes;"> </span>I guess
everyone has seen at least one of these 18-minute-ish presentations on topics
that deal with (broadly speaking) Technology, Entertainment or Design. These “ideas
worth spreading” (as they are advertised), are presented during the TED Conference,
an event occurring every year on the US West Coast since 1990. It is thanks to
the development of the internet and video streaming, however, that TED talks have
accessed global fame. The first talks were uploaded in 2006, and in 2012 the
total views passed 1-billion! (According to TED.com, there are now more than
1,600 talks available!) With as famous speakers as Al Gore, Bill Gates or Bono,
TED talks have become an unprecedented cultural phenomenon. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Today TED
conferences are organized not only in the US, but also in Canada, in South
America, in Europe and in Asia. More than this, TED has become a label, since
all over the world are organized so-called TEDx events, conferences that share
the TED format but are organized by independent local committees. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Given the
format and the varied audience, TED talks are not meant to treat a topic
exhaustively and should be accessible to the layman. This is not necessarily an
easy job for scientists, still you can find almost four hundreds science talks
on the TED website! It seems thus that science fares pretty well in the TED
universe… </span></div>
<div class="MsoNormal">
<br />
<a name='more'></a><br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Take as an
example the excellent presentation of <a href="http://molbio.princeton.edu/faculty/molbio-faculty/31-bassler">Bonnie Bassler</a>, from Princeton University, on
‘How bacteria “talk”’. In the Science special issue that I mentioned in my
previous post, Bonnie Bassler’s talk served to illustrate good
science communication; I couldn’t agree more!</span></div>
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<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.youtube.com/embed/KXWurAmtf78?feature=player_embedded' frameborder='0'></iframe></div>
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<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Of course
I’m far from having watched all four hundreds presentations, but curious minds
will find in the list such great presenters as Richard Dawkins, Steven Pinker,
Craig Venter, and many more. And, good news, there are several presentations
that deal with microorganisms! (You will find up to eighty talks that mention “bacteria”
at some point or the other.)</span></div>
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<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">TED’s
potential for public outreach is truly enormous, and I think it’s good
that scientists embrace this means of communicating science. But this doesn’t
mean that everything is for the best in TED’s world; a growing number of
criticisms and concerns are darkening the blue sky. For instance, the question
of pseudoscience: TED presenters include people that are identified as
scientists even though they promote ideas that lie at the border of science, or
even stand plainly outside of it. Now the problem is that the public cannot <i>a
priori</i> know who they can trust, and rely on the TED team to select valid speakers. A
good example was documented by the evolutionary biologist Jerry Coyne, who personally
convinced TED to withdraw their support from TEDx talks that arguably dealt with pseudoscience. See for instance Coyne's blog posts <a href="http://whyevolutionistrue.wordpress.com/2013/03/14/a-victory-for-real-science-over-woo-tedx-removes-sheldrake-and-hancock-talks-from-youtube-channel/?relatedposts_exclude=84258">here</a>, <a href="http://whyevolutionistrue.wordpress.com/2013/03/06/tedx-talks-completely-discredited-rupert-sheldrake-speaks-argues-that-speed-of-light-is-dropping/">here </a>and <a href="http://whyevolutionistrue.wordpress.com/2013/03/07/tedx-has-second-thoughts-about-rupert-sheldrakes-talk-asks-viewers-to-weigh-in/?relatedposts_exclude=84191">here</a>. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Another
criticism, which actually could be more worrisome than the former (after all,
Coyne showed that the TED team took action when pseudoscience was concerned),
is that too many TED talks are guilty of oversimplification. This criticism was
recently formulated by Benjamin Bratton, Professor of Visual Arts at UC San
Diego, in <a href="http://www.theguardian.com/commentisfree/2013/dec/30/we-need-to-talk-about-ted">the pages of the Guardian</a> and, interestingly, during a TEDx
conference! In essence, Bratton claims that the promises highlighted in TED
talks don’t hold. Some ideas may be worth spreading, but they will never turn
into something real. I think Bratton has some valid points, and it’s probably
good if TED reflects on these. </span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;"><br /></span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">To conclude on a positive note, there are many great science presentations out there thanks to TED, and it would be a pity not to enjoy them! Oversimplification may exist, but some people will use TED talks as an entry to a topic, and will further look for additional, more detailed information.</span><br />
<br />
<span lang="EN-US" style="mso-ansi-language: EN-US;">[Edit: other criticisms of TED are available for instance in the <a href="http://www.newstatesman.com/martin-robbins/2012/09/trouble-ted-talks">New Statesman</a>, and at <a href="http://www.downloadtheuniverse.com/dtu/2012/06/the-demise-of-guys-why-boys-are-struggling-and-what-we-can-do-about-it-by-philip-zimbardo-and-nikita-duncan-ted-books-ki.html">Download the Universe</a>.]</span></div>
<br />Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com32tag:blogger.com,1999:blog-5916121742642761450.post-82374209677694021592014-01-05T07:30:00.000-08:002014-01-26T05:52:02.810-08:00Communicating science in 2014: Public Outreach<!--[if gte mso 9]><xml>
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<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-axDPTHgEmqA/Usl2mNrXslI/AAAAAAAAAo8/TCf4gpOyVtc/s1600/F1.medium.gif" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="http://2.bp.blogspot.com/-axDPTHgEmqA/Usl2mNrXslI/AAAAAAAAAo8/TCf4gpOyVtc/s320/F1.medium.gif" height="320" width="251" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="http://www.sciencemag.org/content/342/6154.toc">October 2013 issue</a> of <i>Science </i>magazine</td></tr>
</tbody></table>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">A few
months ago, the magazine <i style="mso-bidi-font-style: normal;">Science</i>
published a <a href="http://www.sciencemag.org/content/342/6154.toc">special issue</a> on ‘communication in science’. Indeed, the way
scientists exchange information has evolved considerably in the past decade,
thanks notably to the internet and the rise of the <a href="http://en.wikipedia.org/wiki/Open_access">open access</a> movement.
Conversely, older means of communication still fare pretty well; despite
predictions of extinction, IRL meetings are still flourishing, and so are
printed books…<b style="mso-bidi-font-weight: normal;"> </b>This year, I want thus
to orientate this blog a little more towards questions related to science
communication (internal and external) and how scientists deal with it. So I plan to write several posts
about the way scientists communicate between themselves and with society. Here
I want to start with how scientists communicate to the general public.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Science for the masses</span></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Scientists
today are constantly reminded of their duty to communicate their research to
the public, and are encouraged to do what is called <i style="mso-bidi-font-style: normal;">science outreach</i>. I believe this to be fundamentally a good and a
fair thing, if only because the vast majority of science funding is provided by
the public society via taxes. In addition, and in my view more importantly,
every citizen (as well as society as a whole) gain at a better understanding of
science, this for pragmatic, aesthetic and philosophical reasons. </span></div>
<div class="MsoNormal">
<br />
<a name='more'></a><br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">In a 1963
lecture, legendary physicist <a href="http://www.nobelprize.org/nobel_prizes/physics/laureates/1965/feynman-bio.html">Richard Feynman</a> pointed out that the society he
lived in was a highly technical one. But was it a scientific one? In the sense
that society had acquired a scientific outlook, Feynman noted it was certainly
not<sup>1</sup>. I hold Feynman’s statement to be as true today as it was in
the sixties, maybe even more so. High-tech products are everywhere (transport,
communication, agriculture, entertainment), but most of the times we ignore the
science behind the technology. <i style="mso-bidi-font-style: normal;">As long as
it works, who cares?</i> seems a common thought (to which I also fall prey,
often enough). And technology is not the only issue: public health is also of
great concern, as we live in the years of world pandemics, multiresistant
strains of bacteria, and so on. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">The lack of
understanding of what permits technological development may be disheartening,
but more worrisome to me is how weakly the scientific mindset seems to permeate
the population. Is that the scientists’ fault? I guess partly, but I would
water down this by saying that this is society’s responsibility as a whole. But
maybe I am painting too dark a portrait here. After all, the public is overall
very supportive of scientific research. In the past couple of years, we even have
seen a surprising rush of scientists in popular fiction (think CSI, Big Bang
theory), which is probably a good sign. This means we have to keep up the good
communication work!</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Science outreach in the 21<sup>st</sup> century</span></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">In the past
century, science communication was done in books and magazines, on the radio
and on television. At the end of the 20<sup>th</sup> century came the internet
revolution, and, needless to say, it has changed the game ever since. Scientists
can now express their opinion and showcase their research through websites,
blogs, videos, podcasts, social networks, tweets… you name it. Does every
scientist use all of these new means of communication today? Clearly not, but
many prominent and active scientists have embraced internet and its remarkable
power of <i style="mso-bidi-font-style: normal;">outreach</i>. Let’s see what nice
options are at hand:</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Websites</span></i></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Nowadays,
research groups that don’t have a website are the exception rather than the
rule. I believe that it also helps to make science more personal, as most
websites put forward the actual <i style="mso-bidi-font-style: normal;">people</i> that are doing the research. If they are well done, they should appeal to the
layman as well as the scientist. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Blogs</span></i></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Blogs are
far less numerous than websites, for quite understandable reasons, but there is
nevertheless no shortage of them. Recently, Jonathan Eisen (Professor at UC Davis,
Open Access enthusiast and active blogger) came up with an impressive list of <a href="http://phylogenomics.blogspot.ch/2012/06/collecting-links-to-blogs-that-focus.html">100 blogs focusing on microbiology</a>! We should not underestimate the power of emulation: it is after
reading Jon’s blog and others that I decided that I should embark on the blogging
boat as well. Personally, I enjoy blogging because it forces me to formulate
ideas and reflections, something that I wouldn’t have done if not for web
posting. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Tweets</span></i></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">OK, I admit
I’m rather ignorant here. I know scientists use it, but I’m totally
uninterested in Tweeter. I might be missing something big, here, but well… I
guess I’ll live with it (or rather without it).</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Podcasts</span></i></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Podcasts represent
the perfect blend of the old and the new: radio broadcasting and internet. The
American Society for Microbiology, for instance, is increasingly using<a href="http://www.microbeworld.org/index.php"> podcasts </a>to share information. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Pictures and Videos</span></i></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">The posting
of videos and pictures on the web is on the rise, and more and more of these are
made available to the public with few restrictions (for instance with a
creative commons copyright). Anecdotally, we learned that <a href="http://www.youtube.com/watch?v=Fl4L4M8m4d0">scientists can befunny, and that they like Lady Gaga </a>(but who doesn’t?). </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Wikipedia</span></i></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Despite fair
warnings about the reliability of its information content, one has to admit
that Wikipedia is a fantastic resource! In addition, we know that <i style="mso-bidi-font-style: normal;">everyone</i> is using Wikipedia as a source
of information. Hence, instead of dismissing it, scientists have to make sure
that their domain of expertise is fairly treated, not contaminated with
misinformation, and up to date. This said, I haven’t so far taken part in Wikipedia, but I shall consider this in the future, for the aforementioned reasons. Wikipedia
pages may contain mistakes, but this is true of many other web or paper-based
resources, and at least Wikipedia is a dynamic system that allows multiple
corrections and clarifications.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Books, magazine articles, TV and radio shows, press
releases, etc.</span></i></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Older means
of outreach haven’t become obsolete. Far from it. Actually, in my view the most
efficient and long-lasting ‘communicator’ still remains the printed book. There
are science books that deeply influenced me, in a way that no website could
have done, like Rostand’s “Pensées d’un biologiste”, Dawkins’ “Blind watchmaker”
or Russell’s “Scientific Outlook”, and all three were written for the general public.
What I mean to say is that new and old means of communication are <i style="mso-bidi-font-style: normal;">complementary</i>, and most often not in
competition with each other. I am delighted to see that I can download for free
on my e-reader plenty of science masterpieces that are in the public domain,
thanks to websites such as <a href="http://www.gutenberg.org/">Project Gutenberg</a>. Does that mean I do not buy
books anymore? Not at all. Even better, I will buy more books by contemporary
scientists, since I saved some bucks on the classics!</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">It is also
important that scientists write articles in popular magazines and newspapers.
And here I think that scientists are allowed (and should be encouraged) to go
beyond their strict area of expertise, and express their <i style="mso-bidi-font-style: normal;">opinion</i> as society members. Of course, “scientists” are not exactly
a homogeneous group or lobby, but we share values and an outlook that are worth
spreading. What is true for newspapers also holds for TV and radio broadcasts. <span style="mso-spacerun: yes;"> </span></span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Press
releases organized by scientists and universities are important as well, but in
the light of recent controversies over their content and use (for instance, the
<a href="http://ofbacteriaandmen.blogspot.ch/2012/02/what-news-from-arsenic-life-front.html">arsenic life story</a>), I’d rather leave it aside, or rather save it for a longer
development elsewhere. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<b style="mso-bidi-font-weight: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">Let’s make this age scientific</span></b></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Scientists
have now more communication tools than ever before. So there’s every reason to
be positive about the future of science outreach! To conclude, and to invoke
again Richard Feynman, I wish that we can make our age a little bit more
scientific. There’s a lot to gain for everyone.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<u><span lang="EN-US" style="mso-ansi-language: EN-US;">Notes:</span></u></div>
<div class="MsoListParagraph" style="mso-list: l0 level1 lfo1; text-indent: -18.0pt;">
<span lang="EN-US" style="mso-ansi-language: EN-US; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;"><span style="mso-list: Ignore;">1<span style="font: 7.0pt "Times New Roman";">
</span></span></span><span lang="EN-US" style="mso-ansi-language: EN-US;">1. “<i style="mso-bidi-font-style: normal;">There is no doubt at all that today we have
all kinds of scientific applications which are causing us all kinds of
advantages. And so in that sense it certainly is a scientific age. If you mean
by a scientific age an age in which science is developing rapidly and advancing
fully as fast as it can, then this is definitely a scientific age. […] But if
you mean that this is an age of science in the sense that in art, in
literature, and in people’s attitudes and understandings, and so forth science
plays a large part, I don’t think it is a scientific age at all. You see, if
you take, the heroic age of the Greeks, say, there were poems about the
military heroes. In the religious period of the Middle Ages, art was related
directly to religion, and people’s attitudes toward life were definitely
closely knit to the religious viewpoints. It was a religious age. This is not a
scientific age from that point of view.”</i> <span style="mso-spacerun: yes;"></span>Richard Feynman, quoted from the John Danz
lecture “<i style="mso-bidi-font-style: normal;">This unscientific age</i>”, in <i style="mso-bidi-font-style: normal;">The meaning of it all</i> (2007), Penguin
books, pp. 62-63.</span></div>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com0tag:blogger.com,1999:blog-5916121742642761450.post-11350241122042328352013-12-22T05:12:00.002-08:002014-01-05T07:44:03.166-08:00The Invisible Gorilla by Chabris and Simons<!--[if gte mso 9]><xml>
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<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-JQ9j5aq8c6M/UrbkSEcqFFI/AAAAAAAAAoo/cXl1SJeWzJ0/s1600/the-invisible-gorilla-072242721.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="320" src="http://1.bp.blogspot.com/-JQ9j5aq8c6M/UrbkSEcqFFI/AAAAAAAAAoo/cXl1SJeWzJ0/s1600/the-invisible-gorilla-072242721.jpg" width="209" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><a href="http://www.theinvisiblegorilla.com/international.html">UK edition, published by Harper</a></td></tr>
</tbody></table>
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;"></span></i><a href="http://www.theinvisiblegorilla.com/international.html"><i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">The invisible gorilla and other ways ourintuition deceives us</span></i></a><span lang="EN-US" style="mso-ansi-language: EN-US;">,
by psychologists <a href="http://www.chabris.com/">Christopher Chabris </a>and <a href="http://www.dansimons.com/">Daniel Simons</a>, is a wonderful book
that contains a lot of food for thought for scientists – and actually for <i style="mso-bidi-font-style: normal;">everybody</i>. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">There is
little chance that you missed this viral video, dating back from just before
the turn of the millennium: two teams, dressed either in white or in black,
play basketball, and you are supposed to count how many passes the white team
manages to do. If you never saw that, watch it <a href="http://www.theinvisiblegorilla.com/videos.html">here </a>before reading. OK, that
was the one and only spoiler alert!</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">In the
middle of the video, a student wearing a gorilla suit walks through the
players, thumps her chest, and leaves. I didn’t see the gorilla, just as half
of the people who watch the video, because I was too focused on counting the
white team passes. With this video, Chabris and Simons showed us that we
wrongly take certain things for granted, such as our ability to notice
everything that enters our field of view. They write in their introduction (p.
ix):</span></div>
<br />
<blockquote class="tr_bq">
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<span lang="EN-US" style="mso-ansi-language: EN-US;">“We all
believe that we are capable of seeing what’s in front of us, of accurately
remembering important events from our past, of understanding the limits of our
knowledge, of properly determining cause and effect. But these intuitive
beliefs are often mistaken ones that mask critically important limitations on
our cognitive abilities.”</span></div>
</blockquote>
<br />
<a name='more'></a><br /><br />
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">In addition
to discussing the “illusion of attention” (our false belief that we should have
noticed the gorilla), the book covers five other common illusions to which we
fall prey: memory, confidence, knowledge, cause and potential.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">All these
illusions exist because we most often misunderstand the way our brain works. What
hides inside of our skull is no sophisticated computer that “saves” all kinds
of information on some kind of “hard drive”. Actually, scientists and philosophers are still struggling
to understand what it is exactly that the brain does. But it seems to be a
highly dynamic processing machine, which constantly integrates information to
build a useful picture of our surrounding world.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Memory is
particularly treacherous, as our memories evolve and are transformed with time,
without necessarily losing of their veracity feeling. (This can lead to amazing
memory mistakes: the authors bring the story of Hilary Clinton
remembering a mission to Bosnia, and <a href="http://www.theguardian.com/commentisfree/2008/mar/25/clintonunderfire">its heavy consequences on her 2008 campaign</a>.)</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Of specific
interest for scientists are the so-called “illusion of knowledge” and “illusion
of cause”. As to knowledge, it is our tendency to believe that we understand more
than we actually do. The illusion of knowledge can be dramatically exemplified in
fund traders, who believe they “understand” the market and the forces that
govern it, whereas most of the time their gains or losses are just due to
chance. As to cause, the mistake is to believe that when two events happen
together, one must have caused the other; for scientists, this translates into
the popular catchphrase <i style="mso-bidi-font-style: normal;">correlation does
not imply causation</i>. </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Overall, <i style="mso-bidi-font-style: normal;">the invisible gorilla</i> makes for a very engaging
and inspiring book, even though it (sometimes painfully) points out how limited
we human beings can be. The lesson is clear: we have to better understand the
way our cognitive system works to avoid these powerful illusions. This is
enlightening.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<u><span lang="EN-US" style="mso-ansi-language: EN-US;">Reference:</span></u></div>
<br />
<ul>
<li><u><span lang="EN-US" style="mso-ansi-language: EN-US;"></span></u><span lang="EN-US" style="mso-ansi-language: EN-US;">Chabris C. and D. Simons. (2010) <a href="http://www.theinvisiblegorilla.com/international.html"><i>The invisible gorilla and other ways our intuition deceives us</i></a>. Harper Collins. 306 pages (paperback edition, 2011).</span></li>
</ul>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com0tag:blogger.com,1999:blog-5916121742642761450.post-4488267913220869012013-11-04T12:16:00.001-08:002014-01-05T07:43:35.951-08:00Modelling the bacterial colonization of leaves<!--[if gte mso 9]><xml>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-Xh5qoXuXVqU/Unf4ucZcwfI/AAAAAAAAAnI/ANkBF3LaGNM/s1600/Jan1.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="http://1.bp.blogspot.com/-Xh5qoXuXVqU/Unf4ucZcwfI/AAAAAAAAAnI/ANkBF3LaGNM/s400/Jan1.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Photo courtesy of Jan Tech</td></tr>
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<![endif]--><span lang="EN-US" style="mso-ansi-language: EN-US;">Our world
is a quite green world: a sea of trees, bushes, grasses, or, if you happen to
live in the Midwest, corn fields… What is less obvious, though, is the fact
that this green vastness harbors a huge community of microbes. Yeasts and
filamentous fungi are often found on plant surfaces, but the most numerous
inhabitants are first and foremost bacteria. Indeed, a centimeter square of
leaf can contain as many as 10 millions of them! No worries, most of them are
harmless to us or their plant hosts. On the contrary, many are required to
maintain a healthy plant environment, by stimulating plant growth or by
preventing the plant colonization by pathogens (they compete for the same space
and the same resources). </span><br />
<br />
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<span lang="EN-US" style="mso-ansi-language: EN-US;">Because
plants are so vital to us (think food, raw materials, landscapes, etc.), there
is a real interest in understanding what the microbial contribution to the
plant ecosystem is. One lingering question, for instance, is how bacteria colonize
the surface of leaves (what we call the <a href="http://en.wikipedia.org/wiki/Phyllosphere">phyllosphere</a>). What we do know is that bacteria on leaf surfaces appear as clusters of cells, rather than an even layer of bacteria covering the
surface; the mechanisms that lead to this colonization pattern, however, is not
well understood. I have already written about this question <a href="http://ofbacteriaandmen.blogspot.ch/2012/03/mechanics-of-bacterial-cluster.html">in a previous post that dealt with the use of bacterial bioreporters</a>. Another way to explore these
mechanisms of cluster formation is computer-based modelling, which enables us
to test different scenarios and compare it with what has been observed on real
plants. </span><br />
<span lang="EN-US" style="mso-ansi-language: EN-US;"></span><br />
<a name='more'></a><span lang="EN-US" style="mso-ansi-language: EN-US;"><br /></span></div>
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-QF-E999pey8/UnafOXZBfRI/AAAAAAAAAm4/d41le7s7s5c/s1600/LeafBacteria2.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="220" src="http://4.bp.blogspot.com/-QF-E999pey8/UnafOXZBfRI/AAAAAAAAAm4/d41le7s7s5c/s400/LeafBacteria2.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Bacteria (in green) colonize the surface of a snap bean leaf and form clusters. </td></tr>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">In <i style="mso-bidi-font-style: normal;">Explaining bacterial dispersion on leaf
surfaces with an individual-based model</i>, a new study that I co-authored
with <a href="https://www.nioo.knaw.nl/users/avanderwal">Annemieke van der Wal</a> (lead author), <a href="http://www.birmingham.ac.uk/schools/biosciences/staff/profile.aspx?ReferenceId=6059">Jan-Ulrich Kreft</a>, <a href="https://www.nioo.knaw.nl/users/wmooij">Wolf Mooij</a> and
<a href="http://plantpathology.ucdavis.edu/faculty/Leveau_Johan_HJ/">Johan Leveau</a>, we present a computer simulation that helps explain how bacteria
can colonize the surfaces of plant leaves. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075633">It’s just fresh out of the (virtual) press here at PLoS ONE</a>! </span></div>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">To predict
the clustering of bacteria growing on a surface, Annemieke has created a
so-called individual-based (or <a href="http://en.wikipedia.org/wiki/Agent-based_model">agent-based</a>) model<sup>1</sup>. It differs from
a ‘classical’ model in that it doesn’t try to express the behavior of a whole
population using appropriate mathematical expressions. Instead, a
population pattern emerges from the behavior of individual agents (for instance
bacteria) that obey a few simple rules. In our case, we give the bacteria rules as to how they can grow and form microcolonies. The advantage of
such models is that they do not impose any predetermined behavior on the
virtual population, but rather allow complexity to be derived from simple,
individualistic actions.</span></div>
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<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-Gv7MDW4spiU/Unf9M2ESk8I/AAAAAAAAAnY/PLy0o0a7JwY/s1600/Tecon1.png" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="320" src="http://1.bp.blogspot.com/-Gv7MDW4spiU/Unf9M2ESk8I/AAAAAAAAAnY/PLy0o0a7JwY/s320/Tecon1.png" width="296" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Bacteria (in green) clustering next to a leaf stomate. </td></tr>
</tbody></table>
<span lang="EN-US" style="mso-ansi-language: EN-US;"><span lang="EN-US" style="mso-ansi-language: EN-US;">The main
goal of our model was to explain the clustering patterns of bacteria that were
observed in a classic paper by Jean-Michel Monier and Steve Lindow (2004), from
UC Berkeley. Bacteria can grow on pant leaf surfaces thanks to the availability
of plant sugars such as glucose and fructose. These sugars are located in the
sap, but some of it diffuses from the interior of the plant to the exterior, at least if
water is available on the surface to collect these molecules! For this reason,
the presence of water is a key parameter in our model: if the surface is dry,
bacteria cannot grow! When water is present, sugar is available to the
bacteria; they use it, grow and produce offspring that colonize the surface.
Annemieke thus tested the importance of different ‘waterscapes’ on bacterial
growth, for instance comparing a continuous water film with individual droplets
spread across the leaf surface.</span></span><br />
<br />
<span lang="EN-US" style="mso-ansi-language: EN-US;">The video below shows a simulation of colonization run with our model. The surface is represented in 2D (right side in the video), and the round elements represent droplets of water. When the droplets turn dark, it indicates that the concentration of sugar has increased. Individual bacteria are seen in green. They will consume the sugars (the color in the droplet becomes white), divide and form microcolonies containing many individuals. </span></div>
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<a href="http://3.bp.blogspot.com/-PgmymKnt1TQ/Unf_DAv1UtI/AAAAAAAAAn0/6ibmtmfYrB4/s1600/vanderWal2.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><br /></a></div>
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<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dxU14Y5fUj48tpW7WZB3HpvThX2zqkrc4HWew_pOgpf38cgBt_MBO9ZmnKBZwlsFw2CsY7QAkTiyppRQkI00w' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
<br />
<span lang="EN-US" style="mso-ansi-language: EN-US;">This
mechanism (droplet distribution, sugar diffusion, bacterial growth), however,
was not sufficient to explain the experimental patterns seen by Monier and
Lindow. What was missing was bacterial detachment: when bacteria can detach and
disperse from the microcolony in which they originated (as shown in the video), the model predictions
match the experimental results very accurately! (See figures below.) To say it differently, if
there is no bacterial movement (either active or passive), we cannot explain the
experimental observations, namely that we see some large clusters of thousands
of cells and many smaller clusters of only a couple of cells. </span><br />
<br />
<span lang="EN-US" style="mso-ansi-language: EN-US;"> <table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-pSWgbOdsHUg/Unf-nIcfr_I/AAAAAAAAAng/Oze4TOLYsLI/s1600/vanderWal1.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="277" src="http://3.bp.blogspot.com/-pSWgbOdsHUg/Unf-nIcfr_I/AAAAAAAAAng/Oze4TOLYsLI/s400/vanderWal1.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Experimental results by Monier and Lindow.</td><td class="tr-caption" style="text-align: center;"><br /></td><td class="tr-caption" style="text-align: center;"><br /></td><td class="tr-caption" style="text-align: center;"><br /></td></tr>
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<span lang="EN-US" style="mso-ansi-language: EN-US;"><table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-PgmymKnt1TQ/Unf_DAv1UtI/AAAAAAAAAn0/6ibmtmfYrB4/s1600/vanderWal2.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="277" src="http://3.bp.blogspot.com/-PgmymKnt1TQ/Unf_DAv1UtI/AAAAAAAAAn0/6ibmtmfYrB4/s400/vanderWal2.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Predictions of the model without detachment.</td></tr>
</tbody></table>
</span><br />
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-t572xqWE0io/Unf-wYSqkMI/AAAAAAAAAns/l3p7dl80QNM/s1600/vanderWal3.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="260" src="http://4.bp.blogspot.com/-t572xqWE0io/Unf-wYSqkMI/AAAAAAAAAns/l3p7dl80QNM/s400/vanderWal3.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Predictions of the model with bacterial detachment.</td></tr>
</tbody></table>
<br />
<span lang="EN-US" style="mso-ansi-language: EN-US;">The main finding
of our study was thus that bacterial detachment from clusters (and
re-attachment) is an important mechanism in the colonization of plant leaves,
and potentially in the colonization of other natural and artificial surfaces. This gives us a better view of what it means to live a microbe's life!</span></div>
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<br /></div>
<div class="MsoNormal">
<u><span lang="EN-US" style="mso-ansi-language: EN-US;">Notes:</span></u></div>
<span lang="EN-US" style="mso-ansi-language: EN-US; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";">1. </span></span></span><span lang="EN-US" style="mso-ansi-language: EN-US;">The
model was built in <a href="http://ccl.northwestern.edu/netlogo/">NetLogo</a>, a platform developed at the Northwestern
University (Illinois) that is freely available! </span><br />
<div class="MsoListParagraph" style="mso-list: l0 level1 lfo2; text-indent: -18.0pt;">
<br /></div>
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<u><span lang="EN-US" style="mso-ansi-language: EN-US;">References:</span></u></div>
<ul>
<li><span style="font-family: Symbol; mso-bidi-font-family: Symbol; mso-fareast-font-family: Symbol;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"></span></span></span><span lang="EN-US" style="mso-ansi-language: EN-US;">van
der Wal A., Tecon R., Kreft J.-U., Mooij W. M. and J. H. J. Leveau (2013). <i style="mso-bidi-font-style: normal;"><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075633">Explaining bacterial dispersion on leafsurfaces with an individual-based model (PHYLLOSIM)</a>. </i></span>PLoS ONE 8(10):
e75633. doi:10.1371/journal.pone.0075633. </li>
<li>van der Wal A., and J. H. J. Leveau (2011). <a href="http://onlinelibrary.wiley.com/doi/10.1111/j.1462-2920.2010.02382.x/abstract;jsessionid=613334E3FF44122476B7ADAB41A4864E.f01t03?deniedAccessCustomisedMessage=&userIsAuthenticated=false">Modelling sugar diffusion acrosse plant leaf cuticles: the effect of free water on substrate availability to phyllosphere bacteria. </a>Environmental Microbiology 13(3): 792-797. DOI: 10.1111/j.1462-2920.2010.02382.x</li>
<li><span lang="EN-US" style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-font-size: 10.0pt; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: DE-CH; mso-fareast-theme-font: minor-fareast; mso-hansi-theme-font: minor-latin;">Monier J.-M., and S. E. Lindow (2004). </span><a href="http://aem.asm.org/content/70/1/346.short">Frequency, size, and localization of bacterial aggregates on bean leaf surfaces</a>. Applied and Environmental Microbiology 70(1): 346-355. doi:
<span class="slug-doi" title="10.1128/AEM.70.1.346-355.2004">10.1128/AEM.70.1.346-355.2004</span></li>
</ul>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com2tag:blogger.com,1999:blog-5916121742642761450.post-7682044103198950612013-10-08T13:06:00.001-07:002013-11-04T12:23:14.903-08:00Physics meets Biology: Size!<!--[if gte mso 9]><xml>
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<tr><td style="text-align: center;"><a href="http://3.bp.blogspot.com/-SYDrShCy6-4/UlMsFF8noTI/AAAAAAAAAlc/reiLD0hkBB0/s1600/2160541637_743e52395e.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" src="http://3.bp.blogspot.com/-SYDrShCy6-4/UlMsFF8noTI/AAAAAAAAAlc/reiLD0hkBB0/s1600/2160541637_743e52395e.jpg" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Photo courtesy of <a href="http://www.flickr.com/photos/brendanwood/2160541637/">Brendan Wood</a></td></tr>
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<span lang="EN-US" style="mso-ansi-language: EN-US;">One interesting thing about my new job is that my colleagues are not biologists, but physicists. To some
extent, physics was quite absent from my biology curriculum; of course, as a
freshman in biology I attended physics classes, but they were usually
disconnected from the scope of biology (with some notable exceptions, <a href="http://ofbacteriaandmen.blogspot.ch/2012/10/the-science-and-art-of-david-goodsell.html">such as mentioned in this post</a>). If you think about it, there are reasons for this.
Physics – and chemistry as well, for the matter – are fundamentally different
from biology in the sense that each individual atom or molecule is
undistinguishable from another one of the same kind, whereas in biology, in the
words of Ernst Mayr, each individual is unique. The uniqueness of individuals stands at the core of evolution, since natural selection requires
it to operate. </span></div>
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<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Despite
this observation, it is undeniable that biological organisms live and evolve in
the physical world. In that respect, a lot of what organisms can or cannot do
is under direct control of physical laws. If I want to jump, I’d better
hope that my muscles can counteract the force of
gravitation… Physics is thus intricately associated to biology, and when
biologists forget this fact it can lead to absurd hypotheses or ideas that
could be refuted by a wave of a hand. </span></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">With this
in mind, I have decided to do some more reading about the influence of physics
on biology. And one very savory topic is the one of size! </span></div>
<br />
<a name='more'></a><br /><br />
<blockquote class="tr_bq">
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">The most obvious differences between different
animals are differences of size, but for some reason the zoologists have paid
singularly little attention to them. In a large textbook of zoology before me I
find no indication that the eagle is larger than the sparrow, or the
hippopotamus bigger than the hare, though some grudging admissions are made in
the case of the mouse and the whale. But yet it is easy to show that a hare
could not be as large as a hippopotamus, or a whale as small as a herring. For
every type of animal there is a most convenient size, and a large change in size
inevitably carries with it a change of form.</span></i> </div>
</blockquote>
<blockquote class="tr_bq">
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">J. B. S.
Haldane, <a href="http://irl.cs.ucla.edu/papers/right-size.html">On being the right size</a> (1926)<sup>1</sup></span></div>
</blockquote>
<br />
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">In his
delightful short piece, <a href="http://en.wikipedia.org/wiki/J._B._S._Haldane">J. B. S. Haldane</a> points out some of the constraints that physics
imposes on living beings. One of the most striking examples is the relationship between
surface and volume: if a given animal could be made ten times bigger by a magic
wand, its volume would be multiplied by a factor of 1,000, whereas a section of
its body would be multiplied only by a factor of 100… For this reason, its
bones would have to become 10 times more resistant… or break under the weight
excess. (Sorry, Godzilla, but you would probably break your leg at the first
step.) This
observation of the weight/strength relationship was actually made by Galileo,
as I learned in <a href="http://www.princeton.edu/eeb/people/display_person.xml?netid=jtbonner">John T. Bonner</a>’s very nice book, <i style="mso-bidi-font-style: normal;"><a href="http://press.princeton.edu/titles/8241.html">Why Size Matters</a> </i>(2006). In an illustration from his <a href="http://ebooks.adelaide.edu.au/g/galileo/dialogues/complete.html"><i>Dialogues Concerning Two New Sciences</i></a>, Galileo shows how a bone should increase in thickness more than in lenght to keep performing the same function in larger animals.</span><br />
<br /></div>
<div class="MsoNormal">
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-1k0DIUcWlZ4/UlRbCjaIJyI/AAAAAAAAAls/7pQufcJeJNw/s1600/Bone.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" src="http://1.bp.blogspot.com/-1k0DIUcWlZ4/UlRbCjaIJyI/AAAAAAAAAls/7pQufcJeJNw/s1600/Bone.jpg" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Illustration from Galileo Galilei</td></tr>
</tbody></table>
<span lang="EN-US" style="mso-ansi-language: EN-US;">Bonner expresses this rule by stating
that the strength varies as the weight at the power of 2/3. This explaines why,
for instance, the rhino has short thick legs while those of the gazelle are
slender. The difference is of course even more important between animals whose respective size differs by orders of magnitude. Take, for instance, the ant and the ape shown on top of this post. If both were to fall from the top of a building, the fate of the ape would be seriously compromised, while the ant would probably be unharmed. Conversely, being immerged in water is unremarkable for human beings, while insects can easily be trapped by the surface tension of water, and drown!</span></div>
<div class="MsoNormal">
<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; margin-left: 1em; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-lO4Luoe8dig/UlRf-0uLsAI/AAAAAAAAAl8/8aMOCenlMJQ/s1600/bonner.gif" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="320" src="http://2.bp.blogspot.com/-lO4Luoe8dig/UlRf-0uLsAI/AAAAAAAAAl8/8aMOCenlMJQ/s320/bonner.gif" width="247" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Published at <a href="http://press.princeton.edu/titles/8241.html">Princeton University Press</a></td></tr>
</tbody></table>
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">There are
strict limits to what living beings can be, and these limits are physical…
This doesn’t mean, however, that biology cannot find ways around it! Take, for
instance, diffusion: Bonner explains that diffusion occurs through surfaces,
and therefore any increase in weight has to be accompanied by a sufficient
increase of exchange surface. By modifiying its shape, an organism can increase
its exchange surface more rapidly than its weight! Haldane notes (op. cit.):</span></div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;"><span lang="EN-US" style="mso-ansi-language: EN-US;">A man, for example, has a hundred square yards
of lung. Similarly, the gut, instead of being smooth and straight, becomes
coiled and develops a velvety surface, and other organs increase in
complication. The higher animals are not larger than the lower because they are
more complicated. They are more complicated because they are larger.</span></i></div>
</blockquote>
<br />
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">Not only
are larger organisms more complicated, but they also live longer! This becomes
obvious when the average size of living beings is plotted against their generation
time, as shown in the figure below, from J. T. Bonner's book:</span><br />
<span lang="EN-US" style="mso-ansi-language: EN-US;"><br /></span></div>
<div class="MsoNormal">
<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/--wffVQfLWCU/UlRhRUu-lsI/AAAAAAAAAmI/SqZAfbrXDBg/s1600/Bonner_figure.png" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="300" src="http://4.bp.blogspot.com/--wffVQfLWCU/UlRhRUu-lsI/AAAAAAAAAmI/SqZAfbrXDBg/s400/Bonner_figure.png" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Figure 32 from <i>Why Size Matters</i>, reproduced with permission of the author</td></tr>
</tbody></table>
<br /></div>
<div class="MsoNormal">
<span lang="EN-US" style="mso-ansi-language: EN-US;">So the solution to eternal life might be to grow in infinite proportions and slow down the metabolism accordingly! (I guess there wouldn't be much to enjoy in this state, but, well, you can't have it both ways!)</span><br />
<br />
<span lang="EN-US" style="mso-ansi-language: EN-US;">Next time,
I will dive into the size that interests me most, the size of microbes! </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<u><span lang="EN-US" style="mso-ansi-language: EN-US;">Notes</span></u></div>
<div class="MsoListParagraph" style="mso-list: l0 level1 lfo1; text-indent: -18.0pt;">
<span lang="EN-US" style="mso-ansi-language: EN-US; mso-bidi-font-family: Calibri; mso-bidi-theme-font: minor-latin; mso-fareast-font-family: Calibri; mso-fareast-theme-font: minor-latin;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"> </span></span></span><span lang="EN-US" style="mso-ansi-language: EN-US;">1. For
anyone looking for good examples of popular science writing, I warmly recommend reading J. B. S. Haldane. He is one
of the greatest writers I have ever read. Haldane wrote a lot of short science
articles for newspapers, and most are available in collections.</span></div>
<div class="MsoListParagraph" style="mso-list: l0 level1 lfo1; text-indent: -18.0pt;">
<br /></div>
<div class="MsoNormal">
<u><span lang="EN-US" style="mso-ansi-language: EN-US;">References:</span></u></div>
<ul>
<li><span lang="EN-US" style="mso-ansi-language: EN-US;">Haldane J.
B. S. (1926). <a href="http://irl.cs.ucla.edu/papers/right-size.html"><i>On being the right size</i></a>. In <i>Possible Worlds </i>(2001)<i>, </i>Transaction Publishers, 312 pages. </span></li>
<li><span lang="EN-US" style="mso-ansi-language: EN-US;">Bonner J. T. (2006). <a href="http://press.princeton.edu/titles/8241.html"><i>Why size matters: From Bacteria to Blue Whales</i></a>. Princeton University Press, 176 pages.</span></li>
</ul>
<br />Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com0tag:blogger.com,1999:blog-5916121742642761450.post-19787546324997256082013-08-28T12:27:00.004-07:002013-08-28T12:40:36.666-07:00A new continent, a new city, a new job<div class="MsoNormal">
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-O85hnHgm3dY/Uh5OZJM9DgI/AAAAAAAAAkg/3vNUj6sYni8/s1600/100_4383.JPG" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="300" src="http://1.bp.blogspot.com/-O85hnHgm3dY/Uh5OZJM9DgI/AAAAAAAAAkg/3vNUj6sYni8/s400/100_4383.JPG" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">City of Zürich, Switzerland</td></tr>
</tbody></table>
<span style="font-size: small;">I did not expect such a long hiatus
on this blog, but here we are: three months since the last post! Although I don’t
plan to blog as frequently as in 2012, I certainly will resume posting every
now and then. </span></div>
<div class="MsoNormal">
<span style="font-size: small;"><br /></span></div>
<div class="MsoNormal">
<span style="font-size: small;">What happened to me during
this three months period is that I left the University of California-Davis and
I moved back to Europe. It was sad to leave California, truly. This is such a
wonderful place, with wonderful people in it. But <i style="mso-bidi-font-style: normal;">All things must pass</i>, as George Harrison used to sing. I am now in
the beautiful city of <a href="http://www.zuerich.com/en/Visitor.html">Zürich</a>, Switzerland (my home country). So, I have mixed
feelings right now: missing California but enjoying the discovery of a new city.</span></div>
<div class="MsoNormal">
<span style="font-size: small;"><br /></span></div>
<div class="MsoNormal">
<span style="font-size: small;">My new job is at the <a href="http://www.ethz.ch/index_EN">SwissFederal Institute of Technology in Zürich</a>; this venerable institution, founded
in 1855, is often ranked as Switzerland’s top university. Initially, the <i style="mso-bidi-font-style: normal;">Eidgenössische Technische Hochschule Zürich</i>
(its official name – you can also say ETH Zürich, or simply ETH, that you
should pronounce Hay-Tay-Ha if you want to be in) was a polytechnic institute,
whose mission, given by the Swiss government, was to educate engineers and
scientists. In 1909, however, ETHZ started to give PhDs and thus became a
university. (Interestingly, Einstein, who is an ETH alumnus, was awarded a PhD
by the University of Zürich. Because at that time, 1905, none were delivered at
ETH!) </span></div>
<div class="MsoNormal">
<br /></div>
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: right; text-align: right;"><tbody>
<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-_PZLcBv4Tqk/Uh5OrzE98tI/AAAAAAAAAko/I3YFRxjdOWo/s1600/100_4322.JPG" imageanchor="1" style="clear: right; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="320" src="http://1.bp.blogspot.com/-_PZLcBv4Tqk/Uh5OrzE98tI/AAAAAAAAAko/I3YFRxjdOWo/s320/100_4322.JPG" width="240" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Main Building of ETH Zürich</td></tr>
</tbody></table>
<div class="MsoNormal">
<span style="font-size: small;">ETHZ has a sister institution
in western Switzerland, the <i style="mso-bidi-font-style: normal;">École
Polytechnique Fédérale de Lausanne</i> (<a href="http://www.epfl.ch/">EPFL</a>), which became a federal institute
in 1969. These two universities belong to what is called the ETH domain,
together with four institutes of applied research: <a href="http://www.eawag.ch/index_EN">EAWAG </a>(aquatic research), <a href="http://www.wsl.ch/index_EN">WSL</a>(forest, snow and landscape), <a href="http://www.empa.ch/plugin/template/empa/3/*/---/l=2/changeLang=true/lartid=/orga=/type=/theme=/bestellbar=/new_abt=/uacc=">EMPA </a>(Material Sciences) and the <a href="http://www.psi.ch/">Paul ScherrerInstitute </a>(Environment and Human Health). </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<span style="font-size: small;">At ETH, I have joined the group
of <a href="http://www.step.ethz.ch/">Soil and Terrestrial Environmental Physics</a>, that is part of the <a href="http://www.usys.ethz.ch/index_EN">Departmentof Environmental Systems Science</a>. I am now part of a research project that aims
at understanding the origins of bacterial diversity in soil. (I won’t give too
many details here, since I plan to write more about it in a future post!) </span></div>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com0tag:blogger.com,1999:blog-5916121742642761450.post-67070359015071562842013-06-09T12:10:00.000-07:002013-10-08T13:30:12.955-07:00Science fiction meets microbiology: Vitals by Greg Bear<!--[if gte mso 9]><xml>
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<tr><td style="text-align: center;"><a href="http://1.bp.blogspot.com/-RXokXPhH3Gs/UbTNXIYBihI/AAAAAAAAAik/oMEX7GazPro/s1600/Vitals.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="320" src="http://1.bp.blogspot.com/-RXokXPhH3Gs/UbTNXIYBihI/AAAAAAAAAik/oMEX7GazPro/s320/Vitals.jpg" width="194" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"></td></tr>
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<br />
<div class="MsoNormal">
I can’t think of many sci fi books in which microbiology is
the core element of the story—actually I can only think of one, the excellent <a href="http://www.michaelcrichton.net/books-andromedastrain-history.html"><i style="mso-bidi-font-style: normal;">Andromeda Strain</i> </a>of Michael Crichton,
which deals with viral infection from outer space. As to <a href="http://www.gregbear.com/">Greg Bear</a>, author of <a href="http://www.gregbear.com/books/vitals.cfm"><i style="mso-bidi-font-style: normal;">Vitals</i></a> (2002), he had the brilliant idea
of putting bacteria on center stage with, as we shall see, pretty good
intuitions. </div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Bear is an accomplished American science fiction writer. His
short story <i style="mso-bidi-font-style: normal;">Blood Music</i> won both a
Nebula and a Hugo Award, and his <i style="mso-bidi-font-style: normal;">Darwin’s
Radio</i> won a Nebula Award for Best Novel in 2000. He’s considered a ‘hard
SF’ writer, since science has a prominent place in his fictions (which is, by
far, not a prerequisite in science fiction). </div>
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<br /></div>
<div class="MsoNormal">
<i style="mso-bidi-font-style: normal;">Vitals</i> tells the
story of twin brothers, Hal and Rob Cousins, who happened to be microbiologists
(the story is mainly told through the point of view of Hal, but we learn about
Rob via another POV character). The Cousins brothers are in their late twenties
and already very successful scientists. Hal had a tenure track position in
Stanford, however, at the beginning of the book we learn that he has been fired
due to a redistribution of resources at Stanford. So now he’s going rogue, that
is, he’s looking for rich patrons to subsidize his research and he's renting lab
space for his own use—a situation that I thought unrealistic, but I read
<a href="http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2013_05_17/caredit.a1300107">something similar recently in <i style="mso-bidi-font-style: normal;">Science</i></a>,
so... Good news for Hal, his trade is the prolongation of human life, a topic
that has the ear of many rich old men. In the first pages of the book we thus
meet Hal on a mission to seek the secret of eternal life in the deep ocean
floor… </div>
<div class="MsoNormal">
<br />
<a name='more'></a><br /></div>
<div class="MsoNormal">
The main idea behind <i style="mso-bidi-font-style: normal;">Vitals</i>
is extremely interesting: the process of human aging is not inevitable, but is
actually the result of the mitochondrial activity in our cells. Mitochondria
never fully gave up their membership to bacterial life, and they communicate
with the myriads of bacteria in and on our body to control some of our
metabolic functions. Aging and death, in that respect, is just a way bacteria
(often referred to as “the little mothers” in the book) renew the human
livestock and keep the best conditions for bacterial life. Quite far-fetched,
of course, but this vision of an almighty microbiome guiding our lives is not
so distant from the scientific view that has developed during the past decade! Today,
it seems that <a href="http://ofbacteriaandmen.blogspot.com/2012/07/are-all-our-modern-health-issues-linked.html">our inner bacteria are responsible for many aspects of our health</a>,
from our weight to our immunity. Even more striking, a brand-new report in
<i>Nature </i>hints at<i> </i><a href="http://www.nature.com/nature/journal/v497/n7450/full/497442a.html">how mitochondria can have a role in the age of the worm </a><i style="mso-bidi-font-style: normal;"><a href="http://www.nature.com/nature/journal/v497/n7450/full/497442a.html">C. elegan</a>s</i>… Good pick, Mr. Bear!</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Science is central in the book, and rather well represented,
but Vitals wants first to be a technological thriller (<i style="mso-bidi-font-style: normal;">à la</i> Crichton). For this reason Hal Cousins soon has to deal with
matters that are hardly scientific but rather related to his mere survival. At the
beginning of the book, in a nicely rendered claustrophobic scene, Hal is in a
small research submarine, several thousands of feet in the deep blue sea, when
his pilot loses his marbles and attacks him. What should have been an exciting
journey through hydrothermal vents on the seafloor turns into a nightmare... </div>
<div class="MsoNormal">
<br /></div>
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Hydrothermal vents actually are a source of wonder for
biologists and microbiologists. The unmistakable voice of David Attenborough explains why<i>:</i></div>
<div class="MsoNormal">
<br /></div>
<div class="separator" style="clear: both; text-align: center;">
<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.youtube.com/embed/BXGF3XS-yAI?feature=player_embedded' frameborder='0'></iframe></div>
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<br /></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
A lot of interesting microbiological research is done, for
instance by Nicole Dubilier at the Max Planck Institute in Bremen, who studies
<a href="http://www.mpi-bremen.de/en/Research_2.html#Section1235">symbiotic bacteria in vent invertebrates</a>. </div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Back to the book, it seems that the world conspires to kill Dr. Cousins, but
why? What we’ll learn is quite a shocking revelation. It happens that bacteria,
not only responsible for controlling our health, can also influence our minds…
Hal and his brother Rob will thus have to contend with a secret and powerful organization,
a former Soviet Union group of scientists who pioneered mind-control with the
help of carefully selected bacteria. Hal and Rob are standing in the way with
their research, and the wrath of the evil-doers will come upon them. It won’t
be easy for our microbiologist heroes!</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Greg Bear does a rather solid job at unfolding the plot,
however, the techno-thriller genre is a very arduous one, so here and there the
mechanics of the story does not work as smoothly as one may wish. Sometimes the
action seems a bit forced, and the characters’ behaviors a bit unlikely. But nothing
really crippling, in my opinion. More important, I enjoyed the sci fi ideas
developed by Bear. He knows what he’s talking about, he has read his share of
Lynn Margulis’ <a href="http://ofbacteriaandmen.blogspot.com/2012/06/endosymbiotic-theory-of-lynn-margulis.html">theory of endosymbiotic evolution</a> and the book of Shapiro and Dworkin,
<a href="http://www.geociencias.unal.edu.co/unciencias/data-file/user_29/file/Libro.pdf"><i style="mso-bidi-font-style: normal;">Bacteria as Multicellular Organisms</i> </a>(both
acknowledged a the end of the book). As I said there’s only a few microbiology fiction
out there, so it’s worth giving this one a try!</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<u>Reference:</u></div>
<div class="MsoNormal">
Bear G. (2003) <a href="http://www.gregbear.com/books/vitals.cfm"><i style="mso-bidi-font-style: normal;">Vitals</i></a>. Ballantine Books. 416 pages. [Mass Market Paperback]</div>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com2tag:blogger.com,1999:blog-5916121742642761450.post-42224950711692187542013-05-06T21:38:00.000-07:002013-05-06T21:38:19.388-07:00Adieu, François Jacob<br />
<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-J62hKm0aRtI/UYheU-7Ka0I/AAAAAAAAAiE/izopObWg2Qs/s1600/jacob.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="320" src="http://4.bp.blogspot.com/-J62hKm0aRtI/UYheU-7Ka0I/AAAAAAAAAiE/izopObWg2Qs/s320/jacob.jpg" width="228" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">François Jacob. Source: <a href="http://www.nobelprize.org/nobel_prizes/medicine/laureates/1965/">Nobelprize.org</a></td></tr>
</tbody></table>
<a href="http://www.nobelprize.org/nobel_prizes/medicine/laureates/1965/jacob-bio.html">François Jacob</a> passed away on April 20, at the age of 92. He was one of the greatest biologists of the twentieth century and a very fine science writer. (Incidentally, <a href="http://ofbacteriaandmen.blogspot.com/2013/04/of-flies-mice-and-men-by-francois-jacob.html">my last post</a> was about one of his latest books.) Excellent obituaries can be found online, including a <a href="http://phenomena.nationalgeographic.com/2013/04/21/i-think-ive-just-thought-up-something-important-francois-jacob-1920-2013/">nice piece written by Carl Zimmer</a>.<br />
<br />
Jacob's scientific merits are immense, but it is another aspect of his life that struck me when I discovered more about him in the days following his death. (I read the information below in the post by Zimmer and in an <a href="http://www.defense.gouv.fr/salle-de-presse/communiques/ministre-delegue-aupres-du-ministre-de-la-defense-charge-des-anciens-combattants/deces-de-francois-jacob-compagnon-de-la-liberation">obituary by the French Ministry of Defense</a>.)<br />
<br />
In 1940, Jacob joined the French liberation army in England - he was only twenty. Since he was a medical student he served as a medic, participating to campaigns in African countries. Several times he brought back wounded soldiers under enemy fire, and was wounded himself.<br />
<br />
In 1944 he participated to the assault at Utah Beach in Normandy, and a week later he was severely wounded (his arm and his leg) while helping the injured. He was then evacuated to Paris, and was demobilized in 1945.<br />
<br />
Jacob finished his medical studies after the war; he wanted to become a surgeon. His wounds, however, prevented him to do so and he turned to biology and research. Needless to say, François Jacob made the best (and more!) of this forced career reconversion. <br />
<br />
Jacob was not only a brilliant scientist, he was also a brave man who fought to free his country. May he rest in peace.<br />
<br />
<br />Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com0tag:blogger.com,1999:blog-5916121742642761450.post-82711547547582673432013-04-07T15:48:00.003-07:002013-05-06T21:39:54.049-07:00Of Flies, Mice, and Men by François Jacob<!--[if gte mso 9]><xml>
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<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-qeMPQrcXT3U/UWDPiciy3hI/AAAAAAAAAhk/iX7_KnqsgWQ/s1600/3487226.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="320" src="http://4.bp.blogspot.com/-qeMPQrcXT3U/UWDPiciy3hI/AAAAAAAAAhk/iX7_KnqsgWQ/s320/3487226.jpg" width="212" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Published by Harvard University Press</td></tr>
</tbody></table>
<div class="MsoNormal">
It is thanks to <a href="http://www.nobelprize.org/nobel_prizes/medicine/laureates/1965/jacob-bio.html" target="_blank">François Jacob</a> that I began to understand
what evolution meant at the molecular level, when I read his wonderful book <i style="mso-bidi-font-style: normal;">Le jeu des possibles </i>(<i style="mso-bidi-font-style: normal;">The possible and the actual</i>), more than
ten years ago. And “Evolution is tinkering”, Jacob’s catchphrase, is with me
ever since. </div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Jacob, now 92 years old, began his scientific career after fighting
in World War II, and studied lysogenic phages in bacteria at the Pasteur
Institute in Paris. There he met <a href="http://www.nobelprize.org/nobel_prizes/medicine/laureates/1965/monod.html" target="_blank">Jacques Monod</a>, starting one of the most
fruitful collaboration of the 20<sup>th</sup> century. Their work on genetic
regulation in <i style="mso-bidi-font-style: normal;">E. coli</i> culminated in a
Nobel Prize in 1965. In addition to their revolutionary contribution to
molecular biology, Jacob and Monod also wrote books of great importance and large
outreach, notably <i style="mso-bidi-font-style: normal;">Chance and necessity</i>
(Monod) and <i style="mso-bidi-font-style: normal;">The logic of life</i>
(Jacob).<span style="mso-spacerun: yes;"> </span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Of flies, mice, and men<sup>1</sup> (1998) is his last book
to date, a personal journey across biology that spans several decades. The
different chapters feel a little bit disconnected, because apparently they were
first written as lectures for different occasions, but the book is very
enjoyable. Jacob is one of these great scientific figures with a real literary
culture, one who can invoke Dino Buzzatti and ancient greek myths, the poets
Paul Valéry and John Keats, or Tolstoy. </div>
<div class="MsoNormal">
<br />
<a name='more'></a><br /></div>
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In the first chapter, <i style="mso-bidi-font-style: normal;">The
importance of the unpredictable</i>, Jacob offers a plea in favor of
fundamental research, and he tells a striking anecdote about the importance of
emerging sciences: When <a href="http://en.wikipedia.org/wiki/Charles_de_Gaulle" target="_blank">Charles De Gaulle</a>—the leader of French opposition
during WWII, and the first French president after the end of the war—came back
to public office in 1958, he met with a group of scientists to decide what
fields would primarily be funded. A representative of each scientific
discipline was given five minutes to make their case. One proposed the newborn
and promising discipline of molecular biology. Jacob quotes the words of De
Gaulle at the end of this reunion (p.15):</div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
“You might think that a general would be particularly
appreciative of spectacular projects whose descriptions he understands, whose
perspective he shares, and whose developments, consequences, and repercussions
he readily anticipates. Examples among those I’ve just heard would be renewable
energy resources, the conquest of space, and the exploitation of the oceans.
But deep down, I wonder whether this mysterious molecular biology, of which I
know nothing and will certainly never understand anything, isn’t the most
promising of the mid-term developments—unpredictable, rich, capable of doing
much to advance our understanding of the basic phenomena of life and its
disorders. Perhaps it will be the basis for a new medicine that we cannot even
imagine today. It might even be the medicine of the twenty-first century.”</div>
</blockquote>
<br />
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What a foresight! What a lesson!</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Jacob had been extremely successful with the study of
bacteria, and he could have gone on with it for the rest of his career, but in
the mid-sixties he felt that he needed a change. What interested him was
embryonic development, and to study it he must abandon bacteria and select a
new model organism. This is not an easy move at all! Personally, I do not know
any scientist who made such a move in her career. Why is it so? As Jacob put it
(p.53), “over time you become a sort of captive of what you have done and what
you know. Equipment and other paraphernalia—mutants, enzymes, purified products,
all of great value—pile up“. But Jacob decided to make this sacrifice, and to
pick up a new organism. It could have been the fruit fly <i style="mso-bidi-font-style: normal;">Drosophila</i>, or the worm <i style="mso-bidi-font-style: normal;">Caenorhabditis
elegans</i>, but finally it would be the mouse. And he kept working on until now.</div>
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<br /></div>
<div class="MsoNormal">
In addition to guiding us through the history of modern
biology, Jacob has many interesting things to say about the philosophy of
science. Here’s what he writes about our discipline (p.75):</div>
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<blockquote class="tr_bq">
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“Biology admits of a great many generalizations, but very
few theories [As opposed to physics]. The most important among these is the
theory of evolution, because it unites, from a variety of domains, a mass of
observations that would otherwise remain isolated; because it links within
these domains all the disciplines that concern living beings; because it brings
order to the extraordinary variety of organisms—in short, because it supplies a
causal explanation of the living world and its heterogeneity. It’s curious that
the theories of physics such as relativity or quantum theory, which are not
understood by the public, are neither debated nor contested. With the theory of
evolution, it’s the reverse. Everyone thinks they understand it. This theory <i style="mso-bidi-font-style: normal;">is</i> controversial, though challenges to
it are often based on reasons that are irrelevant.”</div>
</blockquote>
<br />
<div class="MsoNormal">
Jacob also goes after some of the myths about scientists and
the scientific method. He thus distinguishes between “day” and “night” science
(p.126):</div>
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<blockquote class="tr_bq">
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“Conscious of its progress, proud of its past, sure of its
future, day science advances in light and glory.</div>
<div class="MsoNormal">
“By contrast, night science wanders blind. It hesitates,
stumbles, recoils, sweats, wakes with a start. […] There is no way to predict
whether night science will ever become day science; whether the prisoner will
emerge from the darkness.”</div>
</blockquote>
<br />
<div class="MsoNormal">
Day science is, of course, what we like to present to the
public. But the public would better understand the unpredictability of research
if it could grasp the reality of night science. As Jacob points out, when we
present scientific results (for instance in scientific articles), we get rid of
all the hesitation and stumbling, this for good reasons. The truth is that
scientific discovery is not a straightforward process at all! Jacob writes,
p.130:</div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
“It is popularly believed that to do scientific work, one
need only observe and accumulate experimental results until a theory emerges
from them. Nothing of the sort. One can contemplate an object form every angle
for years, and never produce any observation of the least scientific interest.”</div>
</blockquote>
<br />
<div class="MsoNormal">
Observations are important in science, but science is by no
means a mere collection of observations. You need to instill some ideas in
there. This is what Max Planck called the ‘metaphysical’ component of science,
in the sense that you need something beyond facts and observations to do
science: hypotheses, theories, etc. </div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Let’s give the final word to Jacob, who is such a wonderful
writer (p.139):</div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
“As in literature or in painting, there is style in science.
Not only a way at looking at the world, but also a way of questioning it.”</div>
</blockquote>
<br />
<div class="MsoNormal">
<u>Notes</u></div>
<div class="MsoNormal">
<span lang="FR-CH" style="mso-ansi-language: FR-CH;">1. <a href="http://www.odilejacob.fr/catalogue/sciences/genetique/souris-la-mouche-et-l-homme_9782738108364.php" target="_blank">Lasouris, la Mouche et l’Homme</a>. Editions Odile Jacob, 1997.</span></div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<u>References</u></div>
<ul>
<li>Jacob F. 1998. <a href="http://books.google.com/books/about/of_Flies_Mice_and_Men.html?id=8rvXWwx7ydQC" target="_blank">Of Flies, Mice, and Men</a>. Translated by Giselle Weiss. Harvard University
Press, Cambridge, 158 pages.</li>
</ul>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com2tag:blogger.com,1999:blog-5916121742642761450.post-13208459807034412762013-03-17T11:12:00.001-07:002013-04-07T16:34:44.789-07:00The Naked Ape by Desmond Morris<table cellpadding="0" cellspacing="0" class="tr-caption-container" style="float: left; margin-right: 1em; text-align: left;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-vOI95967N1Y/UUKK3KgN81I/AAAAAAAAAgU/TI3iAoLod-U/s1600/Naked+ape.jpg" imageanchor="1" style="clear: left; margin-bottom: 1em; margin-left: auto; margin-right: auto;"><img border="0" height="400" src="http://2.bp.blogspot.com/-vOI95967N1Y/UUKK3KgN81I/AAAAAAAAAgU/TI3iAoLod-U/s400/Naked+ape.jpg" width="268" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">First American edition, 1967</td></tr>
</tbody></table>
<i>"There are one hundred and ninety-three living species of monkeys and apes. One hundred and ninety-two of them are covered with hair. The exception is a naked ape self-named</i> Homo sapiens<i>. This unusual and highly successful species spends a great deal of time examining his higher motives and an equal amount of time studiously ignoring his fundamental ones. He is proud that he has the biggest brain of all primates, but attempts to conceal the fact that he also has the biggest penis, preferring to accord this honour falsely to the mighty gorilla. He is an intensely vocal, acutely exploratory, over-crowded ape, and it is high time we examined his basic behaviour."</i><br />
<br />
Desmond Morris is a wonderful writer, and I think this shows in the first paragraph of his best-seller book "<a href="http://entertainment.time.com/2011/08/30/all-time-100-best-nonfiction-books/slide/the-naked-ape-by-desmond-morris/" target="_blank">The Naked Ape</a>" (1967), reproduced above. I hadn't read it for at least ten years, and this second reading (but first time in English) was as enjoyable as the first one.<br />
<br />
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</xml><![endif]--><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">—</span>subtitled <i>A zoologist's study of the human animal</i>—is Morris' attempt to teach us some anthropological and biological facts about ourselves, and this in a very clear and funny way. Morris is a British scientist who studied animal behavior at Oxford. He later worked at the London zoo and he has participated to many radio and television programs. Last but not least, he's the author of many popular science books! (You can read his full biography and find his complete works on <a href="http://www.desmond-morris.com/" target="_blank">his personal website</a>.)<br />
<br />
<a name='more'></a><br /><br />
The book's chapters focus on large topics that deal with our nature: origins, sex, rearing, exploration, fighting, feeding, comfort, with the last chapter being on our interactions with other animals. The main point made by Morris in his book is that the human animal<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">—</span>a term also popularized by the great biologist <a href="http://en.wikipedia.org/wiki/Jean_Rostand" target="_blank">Jean Rostand</a><span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">—</span>has evolved from an ancestor ape, and that this heritage still very much shows in our day-to-day behavior. He writes that "<i>it is the biological nature of the beast that has moulded the social structure of civilization, rather than the other way around</i>" (p. 84).<br />
<br />
So, what made us who we are? (<i>I yam what I yam</i>, as the sailor man says.) It seems that a fundamental move was a literal one: from the forest to the savannah, and the subsequent adoption of territoriality and carnivorism, among other things. The body changes, such as the loss of our fur and the upright position, probably originated jointly. A likely mechanism for this evolution is the process of <a href="http://en.wikipedia.org/wiki/Neoteny" target="_blank">neoteny</a>, in which traits present in the young are kept in the adult (a famous example is that young chimpanzees look more like humans than adult chimpanzees). <br />
<br />
We thus live our modern lives in our big cities with bodies and minds that evolved to produce successful apes standing upright and hunting in packs. What we do is of course influenced by our culture, but the part of instinctive behavior is most certainly overlooked<span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; line-height: 115%; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: Calibri; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-latin; mso-hansi-theme-font: minor-latin;">—</span>and this is as true today as it was in the 1960s.<br />
<br />
Morris is at his best when he dissects our modern habits in the light of our prehistoric instincts. I particularly like the following example, and anyone used to giving public
presentations will I'm sure feel better after reading it (p.164):<br />
<blockquote class="tr_bq">
"Only
a truly aggressive individual can fix you in the eye for any length of
time. [...] A professional lecturer takes some time to train himself to
look directly at the members of his audience, instead of over their
heads, down at his rostrum, or out towards the side or back of the hall.
Even though he is in such a dominant position, there are so many of
them, all staring (from the safety of their seats) at him, that he
experiences a basic and initially uncontrollable fear of them." </blockquote>
And this one about housings and territoriality (p.183):<br />
<blockquote class="tr_bq">
"One of the important features of the family territory is that it must be easily distinguished in some way from all the others. [...] This is something which seems obvious enough, but which has frequently been overlooked or ignored, either as a result of economic pressures, or the lack of biological awareness of architects. Endless rows of uniformly repeated, identical houses have been erected in cities and towns all over the world. [...]The psychological damage done to the territorialism of the families forced by architects, planners and builders to live under these conditions is incalculable."</blockquote>
Other great and funny examples of ancient behaviors applied to modern life include the use of submission gestures to appease a policeman after having been pulled over (Morris tried it first-hand!), and the remarkable stability of our number of acquaintances, even in crowded cities, which approximates the size of a small tribe!<br />
<br />
If Morris insists on our animal nature and our limitations, it is to help us "<i>to keep a sense of proportion and to force us to consider what is going on just below the surface of our lives</i>". He also acknowledges that we have great merits, of course, but since their is no shortage of praise for our species in other books, his aim is not to add on this. He beautifully concludes "The Naked Ape" as follows (p.241):<br />
<blockquote class="tr_bq">
"We must somehow improve in quality rather than in sheer quantity. If we do this, we can continue to progress technologically in a dramatic and exciting way without denying our evolutionary inheritance. If we do not, then our suppressed biological urges will build up and up until the dam bursts and the whole of our elaborate existence is swept away in the flood."</blockquote>
To read more about Desmond Morris, this <a href="http://ofbacteriaandmen.blogspot.com/2012/05/human-zoo-by-desmond-morris.html" target="_blank">previous post is about "The Human Zoo"</a>, the follow-up of the Naked Ape, which focuses on the social relations of our species. A recent and brilliant piece by Morris, written on the occasion of Darwin's bicentennial, is available on the <a href="http://www.dailymail.co.uk/news/article-1101985/Two-centuries-salute-Charles-Darwin-Hero-age.html" target="_blank">Daily Mail website</a>. <br />
<br />
<u>References:</u><br />
<ul>
<li>Morris D. (1967) The Naked Ape. McGraw-Hill, New York. 252 pages. </li>
</ul>
<br />
<br />
<br />
<br />
<br />
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<![endif]--><br />Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com0tag:blogger.com,1999:blog-5916121742642761450.post-25441217990307994402013-03-09T18:56:00.001-08:002013-03-17T11:13:02.999-07:00Fluorescent bacteria under the microscope<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://4.bp.blogspot.com/-7kzS2wDIgfQ/UTlr0uWu9eI/AAAAAAAAAes/K8l4IM_pL4A/s1600/63x_T20h_20_modif_crop.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="207" src="http://4.bp.blogspot.com/-7kzS2wDIgfQ/UTlr0uWu9eI/AAAAAAAAAes/K8l4IM_pL4A/s400/63x_T20h_20_modif_crop.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;"><i>Pantoea agglomerans </i>and <i>Pseudomonas syringae</i> bacteria</td></tr>
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Some time ago I made experiments growing two bacterial species on a gel surface, using fluorescence to distinguish between them. Since some of these pictures looked nice to me, I decided to share them here!<br />
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Here's some information about the bacteria and how the images were taken:<br />
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<i>Pantoea agglomerans</i> and <i>Pseudomonas syringae</i> are two bacterial species that live in association with plants: the former as a harmless inhabitant of plant leaves and the latter as a pathogen that can colonize the inside part of the plants. Because it is not easy to visualize these bacteria in their natural environment (the surface of plant leaves), it is common to use fluorescently-tagged strains. I discussed this type of research <a href="http://ofbacteriaandmen.blogspot.com/2012/03/mechanics-of-bacterial-cluster.html" target="_blank">in a previous post</a>.<br />
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In this case, <i>P. agglomerans</i> expressed the green fluorescent protein (GFP), while <i>P. syringae</i> expressed the red fluorescent protein (DsRed). Hence the colors that are displayed in the pictures are only pseudo-colors produced by the image analysis software. There's a good reason for that: I take black & white pictures! The red and green fluorescence were recorded sequentially, as we have to use different filters to capture one or the other. What is presented is a merged image, a reconstruction of the scene based on two distinct pictures. In contrast, the grayscale image is a phase contrast image that captured the two species simultaneously. <br />
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The bacteria grew on the surface of a nutrient gel medium, and they are at a stage where many of them form a single layer of cells on the gel surface (every area where you can distinguish individual bacteria). When the fluorescence intensity is higher and the details are blurred, it means that several layers of bacteria are sitting on top of each other. <br />
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The two bacterial species are morphologically distinct: <i>Pseudomonas syringae</i> form longer rods than <i>Pantoea agglomerans</i>. The fluorescence greatly enhances the distinction between the two, and this is useful in studies that aim at studying the proportion and distribution of different bacterial species in natural environments. <br />
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<br />Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com2tag:blogger.com,1999:blog-5916121742642761450.post-47645978119577210272013-02-24T11:48:00.002-08:002013-03-17T11:14:52.636-07:00Where have all the geniuses gone?<!--[if gte mso 9]><xml>
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<table align="center" cellpadding="0" cellspacing="0" class="tr-caption-container" style="margin-left: auto; margin-right: auto; text-align: center;"><tbody>
<tr><td style="text-align: center;"><a href="http://2.bp.blogspot.com/-DPbFryFolz4/USr-GchUCpI/AAAAAAAAAeU/lBlJXwHCi1s/s1600/640px-Nernst,_Einstein,_Planck,_Millikan,_Laue_in_1931.jpg" imageanchor="1" style="margin-left: auto; margin-right: auto;"><img border="0" height="286" src="http://2.bp.blogspot.com/-DPbFryFolz4/USr-GchUCpI/AAAAAAAAAeU/lBlJXwHCi1s/s400/640px-Nernst,_Einstein,_Planck,_Millikan,_Laue_in_1931.jpg" width="400" /></a></td></tr>
<tr><td class="tr-caption" style="text-align: center;">Nernst, Einstein, Planck, Millikan and Laue in 1931. From <a href="http://commons.wikimedia.org/wiki/File:Nernst,_Einstein,_Planck,_Millikan,_Laue_in_1931.jpg" target="_blank">Wikimedia commons</a>.</td></tr>
</tbody></table>
<div class="separator" style="clear: both; text-align: center;">
</div>
<br />
<div class="MsoNormal">
Is scientific genius gone for good? No more Darwin or
Einstein on the horizon? That’s the intriguing and slightly provocative
question recently raised by UC Davis psychologist <a href="http://psychology.ucdavis.edu/Simonton/" target="_blank">Dean Keith Simonton</a> in the
<a href="http://www.nature.com/nature/journal/v493/n7434/full/493602a.html" target="_blank">comment section of the journal <i style="mso-bidi-font-style: normal;">Nature</i></a>.
Simonton has extensively written on the topic of science creativity in books
and articles, and here’s how he sums up the problematic:</div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
“Geniuses have played a decisive part in science in two main
ways. First, they have founded new scientific disciplines […]. Second, geniuses
have revolutionized established disciplines. […] Yet, in my view, neither
discipline creation nor revolution is available to contemporary scientists.”</div>
</blockquote>
<br />
<a name='more'></a><br /><br />
<div class="MsoNormal">
Simonton seems to trace back the last genius to Einstein. After
him, a door was closed... For a century, suggests Simonton, no real new
discipline has emerged. He writes:</div>
<br />
<blockquote class="tr_bq">
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“Future advances are likely to build on what is already
known rather than alter the foundations of knowledge. […] Natural sciences have
become so big, and the knowledge base so complex and specialized, that much of
the cutting-edge work these days tends to emerge from large, well-funded
collaborative teams involving many contributors.”</div>
</blockquote>
<br />
<div class="MsoNormal">
Simonton, however, provides us with a few disclaimers.
Scientific progress is not at an end, he says. Knowledge will continue to
increase. But progress will be made of smaller and smaller increments, just as
today’s athletes break records by thousandths of a second. Simonton also
refuses the possibility that modern scientists are less clever than their colleagues
from the past. In other words, the source of the change is not to be found in
the people, but in the whole scientific frame of our era. Simonton concludes:</div>
<br />
<blockquote class="tr_bq">
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“I am not asserting that brilliant scientists can no longer
attempt to introduce new paradigms, or even to devise original disciplines. It
is just that such innovations seem less likely to catch on.”</div>
</blockquote>
<br />
<div class="MsoNormal">
So, what to do with Simonton’s claims? No more new
scientific disciplines, no more revolutionary ideas to turn our knowledge
upside down, really? Simonton is right to say that the emergence of new
discipline is less and less likely to happen. This is because scientific
discovery does not operate in the void, but rather lies on the accumulated knowledge:
after three centuries of modern science, we have made a lot of progress, and
the unknown is shrinking. This is, of course, good news, even if it means less
striking discoveries in the future. </div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
I’d argue, however, that in his analysis of the past century
Simonton is oblivious of at least one new major discipline: molecular biology. According
to Simonton this wouldn’t count as a <i style="mso-bidi-font-style: normal;">bona
fide</i> new discipline, since you can decompose it into preexisting disciplines
(say, biology, chemistry and physics). But this analysis considerably plays
down the revolutionary impact of molecular biology on our understanding of
life, including its crucial philosophical consequences (these discoveries,
initiated more than fifty years ago, were an almost fatal blow to <a href="http://ofbacteriaandmen.blogspot.com/2012/03/synthetic-life-and-vitalism.html" target="_blank">the doctrine of vitalism</a>). </div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
In addition, I’d argue that the researchers who led this
revolution (for instance Watson & Crick, Monod & Jacob) were geniuses
in their own right! Closer to us, the application of molecular biology (under
the form of DNA sequences) to evolutionary biology by <a href="http://ofbacteriaandmen.blogspot.com/2013/01/the-new-biology-of-carl-woese.html" target="_blank">Carl Woese</a> has led
another scientific revolution, even though its impact still lacks a true
recognition by the public. So I think that, in his analysis of the recent past,
Simonton is a little too prompt at deeming some advances as non-revolutionary.</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
Now what about what lies ahead of us? “Prediction is very difficult,
especially about the future”, as Niels Bohr said (or maybe it was Yogi Berra?).
Simonton is quite aware of that, and he wittily concludes his piece: “It takes
only one new scientific genius to prove me wrong.” Actually, many comments on
the <i style="mso-bidi-font-style: normal;">Nature</i> website pointed this
weakness out. On that topic I’d like to quote another scientific genius, <a href="http://www.nobelprize.org/nobel_prizes/medicine/laureates/1965/jacob-bio.html" target="_blank">François Jacob</a>, from his very nice book “<a href="http://books.google.com/books/about/Of_Flies_Mice_and_Men.html?id=8rvXWwx7ydQC" target="_blank">Of flies, mice and men</a>” (1998), p. 12: </div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
“Yet science is also unpredictable. Research is an endless
process; we can never say how it will evolve. Unpredictability is part of the
very nature of the scientific enterprise. If what we are going to find out is
truly new, then it is by definition something we cannot know in advance. There
is no way to say where a given field of research will lead. This is why we
cannot choose certain aspects of science and reject others.”</div>
</blockquote>
<br />
<div class="MsoNormal">
This said, I think Simonton is right to emphasize that today’s
science is different from that of Einstein at the beginning of the twentieth
century. We live in the era of ‘Big Science’, which favors large science projects
that have carefully planned timetables and outputs (the Large Hadron Collider
is a paramount example). In this type of projects, little is left to unknown
and risky fields. Most national research agencies, however, are aware of this
and fortunately still provide funding for more exploratory science. So I agree
that the situation is unique to our time. Nevertheless, I’m tempted to say that
science <i style="mso-bidi-font-style: normal;">at any time</i> is different from
the science of the past. Look for instance at what Bertrand Russell wrote in
his essential book “<a href="http://books.google.com/books/about/The_Scientific_Outlook.html?id=eLe1Bav9NBcC" target="_blank">The Scientific Outlook</a>” (1931), p. 38:</div>
<br />
<blockquote class="tr_bq">
<div class="MsoNormal">
“The rate of progress in science nowadays is much too great
for such works as Newton’s <i style="mso-bidi-font-style: normal;">Principia</i>,
or Darwin’s <i style="mso-bidi-font-style: normal;">Origin of Species</i>. Before
such a book could be completed, it would be out of date. In many ways this is
regrettable, for the great books of the past possessed a certain beauty and
magnificence which is absent from the fugitive papers of our time, but it is an
inevitable consequence of the rapid increase of knowledge, and must therefore
be accepted philosophically.”</div>
</blockquote>
<br />
<div class="MsoNormal">
In that sense, Einstein (Russell’s contemporary) was a very
different genius from the likes of Darwin or Newton. For this reason, we should
not wait for a new Einstein to come, but rather look forward to someone, or
something, radically different.</div>
<div class="MsoNormal">
<br /></div>
<div class="MsoNormal">
<u>References:</u></div>
<br />
<ul>
<li><span style="font-family: Symbol; mso-bidi-font-family: Symbol; mso-fareast-font-family: Symbol;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"></span></span></span>Simonton, D. K. (2013). <a href="http://www.nature.com/nature/journal/v493/n7434/full/493602a.html" target="_blank">Scientific genius is extinct</a>. <i style="mso-bidi-font-style: normal;">Nature</i> Vol. 493, p.602.</li>
<li><span style="font-family: Symbol; mso-bidi-font-family: Symbol; mso-fareast-font-family: Symbol;"><span style="mso-list: Ignore;"><span style="font: 7.0pt "Times New Roman";"></span></span></span>Jacob, F. (1998). <a href="http://books.google.com/books/about/Of_Flies_Mice_and_Men.html?id=8rvXWwx7ydQC" target="_blank">Of flies, mice and men</a>.
Harvard University Press. 158 pages.</li>
<li>Russell, B. (2001). <a href="http://books.google.com/books/about/The_Scientific_Outlook.html?id=eLe1Bav9NBcC" target="_blank">The Scientific Outlook</a>. Routledge (First published in 1931). 228 pages. <span style="font-family: "Calibri","sans-serif"; font-size: 11.0pt; mso-ansi-language: EN-US; mso-ascii-theme-font: minor-latin; mso-bidi-font-family: "Times New Roman"; mso-bidi-font-size: 10.0pt; mso-bidi-language: AR-SA; mso-bidi-theme-font: minor-bidi; mso-fareast-font-family: "Times New Roman"; mso-fareast-language: EN-US; mso-fareast-theme-font: minor-fareast; mso-hansi-theme-font: minor-latin;"> </span></li>
</ul>
Robin Teconhttp://www.blogger.com/profile/15672357119122183363noreply@blogger.com0