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Genetics

X activity center

1 Comment

A recent editorial in PLoS Biology was about “Sex, dose and equality“. I always had problems to understand X linked recessive disease and carrier status of a woman: If the random X inactivation would have been complete why are there not much more colorblind women? Obviously the second X is at least partially active as a rescue system. Continue reading X activity center →

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Software

More Zotero support

Welcome Just Science Participant! Here is an extra primer how to store your references from the scientific papers that you are reading. In 1983 I was writing on cards, moved to a simple 4-column-database in 1989, used Endnote in 2005 and eventually moved to Zotero in 2007. Zotero is an open source database that sits as a plugin in your Firefox browser [download link]. The neat thing Continue reading More Zotero support →

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Genetics, Philosophy

New psoriasis gene would have been missed by testing linkage only

A recent study published in nature genetics study highlights a ß-defensin gene where increased copy numbers are related to psoriasis. The normal range is 2 – 12 copies with the risk increasing with each extra copy. I don´t know if the given explanation is really correct: more genomic copies lead to more RNA, lead to more antimicrobial peptide, lead to skin inflammation. Maybe there is an unknown intermediate step: more antimicrobial peptide -> induce other inflammtory interleukins -> skin inflammation.
In any case, Continue reading New psoriasis gene would have been missed by testing linkage only →

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Theology

Just Science Week

The Just Science 2008 will start next week – and here is my last chance to say something non scientific: Science is a method, that has certain prerequisites, works under certain conditions while using techniques with strengths and limitations and is leading to certain conclusions evident to some but not all humans. Needless to say that from a protestant / Lutheran view that there are other ways to explain a phenomenon while providing even extra dimensions like giving an ethical justification.

Haldane / When I am dead / 1928: I am not myself a materialist, because, if materialism is true, it seems to me that we cannot know that it is true. If my opinions are the results of a chemical processes going on in my brain, they are determined by the laws of chemistry, not those of logic.

More at the recent immersion blog post…

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Video, Vitamins

A secosteroid transcriptional activator

A new vitamin D review is more serious about the biology and possible outcomes than some others.

The popular press is talking about vitamin D as “The Sunshine Vitamin”, promoting it as capable of reducing the risk of cancers and autoimmune disease. Yet vitamin D is actually a secosteroid transcriptional activator, at the heart of the innate immunity.

This looks trivial but it isn´t if you look at the NEJM paper Continue reading A secosteroid transcriptional activator →

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Philosophy

Write letters – they are important

Scientific correspondence has always been important – as part of the dialectical and hermeneutical process of interpreting data. The value of scientific letters recently dropped for several reasons Continue reading Write letters – they are important →

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Genetics

Zotero Miniserver

1 Comment

Here is a proof of principle project that can be further adjusted to your own needs – a simple server script that can look up your most recent Zotero database entries and display them to the world. When run in a DOS or Linux box as ZoteroServer path/zotero.sqlite it will display the most recent entries to clients listening at localhost:8888. The code should be pretty straightforward and may be replaced with even other items.

ZoteroServer.pl

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82:		# ZoteroMiniServer: show recent Zotero entries
# m@wjst.de 27/1/08
#----------------------------------------------------------------------------------------------
#perl2exe_include "DBI.pm"
#perl2exe_include "DBD/SQLite.pm"
#perl2exe_include "CGI.pm"
#perl2exe_include "IO.pm"
my $dbfile = <$ARGV[0]>;
#----------------------------------------------------------------------------------------------
use DBI;
use CGI;
$dbh = DBI->connect(
"dbi:SQLite:$dbfile",
"",    # no user
"",    # no password
{ RaiseError => 1 },    
) || die "Cannot connect: $DBI::errstr";

my $sql = 'SELECT DISTINCT items.itemID
FROM items
ORDER BY items.dateAdded DESC
LIMIT 50';
$res0 = $dbh->selectall_arrayref($sql);
my $idlist="";
for $i ( 0 .. $#{$res0} ) {
    for $ii ( 0 .. $#{$res0->[$i]} ) {
        # print "$i:$ii:$res0->[$i][$ii]  ";
    }
    if ($i >0 ) {
        $idlist .= ',' . $res0->[$i][0];
    }
    else {
        $idlist = $res0->[0][0];
    }
}
my $itemlist="";
my $sql = 'SELECT DISTINCT itemDataValues.value
FROM items LEFT JOIN itemData ON items.itemID = itemData.itemID LEFT JOIN itemDataValues ON itemData.valueID = itemDataValues.valueID
WHERE items.itemID IN (' . $idlist . ') AND itemData.fieldID=110';
$res1 = $dbh->selectall_arrayref($sql);
my $itemlist1="";
my $itemlist2="";
my $tagA = '<span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rfr_id=info%3Asid%2Focoins.info%3Agenerator&amp;rft.genre=article&amp;rft.atitle=';
my $tagB = '"></span></br>';
for $i ( 0 .. $#{$res1} ) {
    $itemlist1 .= $tagA . CGI::escape($res1->[$i][0]) . $tagB;
    $itemlist2 .= '<li>' . $res1->[$i][0] . '</li>';
}
#----------------------------------------------------------------------------------------------
use IO::Socket;
my $myport=8888;
my $server=IO::Socket::INET->new(LocalPort=>$myport,
    Type=>SOCK_STREAM,
    Reuse=>1,
    Listen=>10);
my $client;
my $client_adress;
my $data;
print "Listening on port $myport ... \n";
while (  ($client,$client_adress) = $server->accept() ) { 
    my( $client_port,$client_iaddr) = sockaddr_in($client_adress);
    my $client_dot_ip = inet_ntoa($client_iaddr);
    my $client_name   = gethostbyaddr($client_iaddr,AF_INET);
    print "Accepting client $client_dot_ip [$client_name] port: $client_port\n";
    $client->recv($data,10000);
    # print "\nReceived from client:\n$data\n" ;
    my $site= "<html>\n";
    $site .= "<head>\n";
    $site .= "<title>ZoteroServer</title>\n";
    $site .= "</head> \n";
    $site .= "<body>\n";
    $site .= "<b>ZoteroMiniserver</b><BR/>\n";
    $site .= "just click the icon in URL bar above to import any of the following references<BR/>\n";
    $site .= '<ol>' . $itemlist2 . '</ol>';
    $site .= $itemlist1;
    $site .= "</body>\n";
    $site .= "\n</html>\n ";
    print $client $site;
    close($client);
}
close $server; 

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Allergy

Atopic march to a dead end

“.. or does the theory really have legs?” is the title of a critical editorial in JMCP last month. Although I will co-author a forthcoming paper on allergic rhinitis being a risk factor for later asthma, the situation is far from being understood. “March” implies a command for all to go into one direction which is arguable a poor analogy Continue reading Atopic march to a dead end →

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Joke

Why blog writing is something different from writing a paper

This may be obvious, at least if you have read Daniel Gilbert

In 2002, Jane Ebert and I discovered that people are generally happier with decisions when they can’t undo them. When subjects in our experiments were able to undo their decisions they tended to consider both the positive and negative features of the decisions they had made, but when they couldn’t undo their decisions they tended to concentrate on the good features and ignore the bad.

When reading my own writings a second time, I always discover typing errors, crude sentences, and other poor habits – blogs as snapshots of less happier minds?

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Genetics

Change your genes

Yahoo news has the story (and Spiegel a video) of an Australian girl who

spontaneously switched blood groups and adopted her donor’s immune system following a liver transplant in the first known case of its type, doctors treating her said Thursday.

Unfortunately Continue reading Change your genes →

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Joke, Theology

Edge Question wrong

Here comes the second comment on the Annual Edge Question 2008.

When thinking changes your mind, that’s philosophy.
When God changes your mind, that’s theology.
When facts change your mind, that’s science.
What have you changed your mind about? Why?

I would have done it in a different way: Continue reading Edge Question wrong →

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Philosophy, Theology

In memory of Peter Lipton

1 Comment

I have been asked to give an evening lecture about science and religion here at a local congregation. At the first moment, I did not want to do that, but finally promised to take up this challenge – there are so many heroes where I could get some inspiration. I remember having read a wonderful paper by an author but could not recall his name. Continue reading In memory of Peter Lipton →

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