On the limits of science

Have you ever heard of the Wikipedia Knowledge Dump? With the headline “WikiDumper: The Official Appreciation Page for the Best of the Wikipedia Rejects. One man’s trash is another man’s treasure” Dr. Cliff Pickover collects the best entries. For example you can read about the Beard Theorem that suggests that the size of one’s beard has a direct correlation to the radicality of a person’s socialist views. The site is as good as the Ig Noble, yea, yea.

Can anybody become a Nobel Prize winner?

Anders Sandberg attended a seminar in Stockholm and has written an interesting report. I have doubts if we have so much need for heroes. There are so many prizes that you can apply for – an impressive list of prizes and honours that you can find at the CVs of some laureates: Albert Lasker Award, Paul Ehrlich Prize, and many, many more. Google returns 60.100.000 hits if you search for “science prize” and there is now even the European database of science prizes that will find a prize for every scientist. Yea, yea.

WordPress as CMS

I have read many useful (and also some less useful) comments how to squeeze WordPress to work as a CMS.

I did not want to make any major changes to scripts that would be lost after an upgrade. I did not want to have extra plugins to change home (for example by creating an overriding home.cfm). I did not want to have any new categories. I did not want to change permalink structure. I still need my directory plugin to work, I still need the blog (some redirects even loose the blog address!) and I wanted to keep the RSS feed.

After several hours I came up with an very simple solution: Take a standard page and rename its title and slug to “Home” – assign a special “Home” template – redirect htaccess to this page. The only trick is to make the “Home” template work: it is basically a copy of the index.cfm in your WordPress theme directory where the line calling loop.php is being replaced with a slightly modifed loop code.

myblog.php

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<?php
/*
Template Name:MyBlog
*/
?>

<?php get_header(); ?>
<?php get_sidebar
(); ?>

<div id="primary">
<?php query_posts('showposts=5'); ?>
<?php 
while(have_posts()) : the_post(); if(!($first_post == $post->ID)) : ?>
    <div class="entry">
        <div class="post-meta">
            <h2 class="post-title" id="post-<?php the_ID(); ?>"><?php if(!is_single()) { ?><a href="<?php the_permalink() ?>" rel="bookmark" title="Permanent Link to <?php the_title(); ?>"><?php the_title(); ?></a><?php } else { the_title(); } ?></h2>
            <p class="post-metadata"><?php the_time('l, F jS'?><?php if(!get_option('tarski_hide_categories')) { ?> in <?php the_category(', '); ?><?php ?><?php /* If there is more than one author, show author's name */ $count_users $wpdb->get_var("SELECT COUNT(*) FROM $wpdb->usermeta WHERE `meta_key` = '" $table_prefix "user_level' AND `meta_value` > 1"); if ($count_users 1) { ?> by <?php the_author_posts_link(); } ?> | <?php comments_popup_link('No comments''1 comment''% comments''''Comments closed'); ?><?php edit_post_link('Edit',' (',')'); ?></p>
        </div>
        <div class="post-content">
            <?php the_content(' more &raquo;&raquo;&raquo;'); ?>
            <p class="tagdata"><?php _e('Tags: '); UTW_ShowTagsForCurrentPost("commalist"?> | <?php _e('Trackback: '); ?>
            <a href="<?php the_permalink() ?>trackback/">link</a></p>
        </div>
    </div>
<?php endif; endwhile; ?>
</div>

<?php get_footer(); ?>

HUGO Changing Offensive Gene Names

Hsien Hsien Lei has a good comment on gene names approved by Human Genome Organisation (HUGO) Gene Nomenclature Committee which are nevertheless offending . Some of the inappropriate names are LFNG – lunatic fringe homolog (Drosophila), MFNG manic fringe homolog (Drosophila) as well as SHH sonic hedgehog homolog (Drosophila). There are many more names that arise only from a particular culture (like death executioner Bcl-2); it seems also a particular kind of humour to call a deaf mouse Beethoven. Yea, yea.

How to set up a proxy in 1 minute

There are many ways to do this – for example by reconfiguring your Apache installation. The fastest procedure, however, is to download DeleGate for your platform and create this batch file

rundelegate.cmd

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@echo off
dg9_2_5.exe -P80 SERVER=http -vd -f ADMIN=your@email.de AUTHORIZER="-list{anyuser:anypassword}"
pause

Our knowledge springs from two main sources

Immanuel Kant is now also online in English language

Our knowledge springs from two main sources in the mind, first of which is the faculty or power of receiving representations (receptivity for impressions); the second is the power of cognizing by means of these representations (spontaneity in the production of conceptions). Through the first an object is given to us; through the second, it is, in relation to the representation (which is a mere determination of the mind), thought. Intuition and conceptions constitute, therefore, the elements of all our knowledge, so that neither conceptions without an intuition in some way corresponding to them, nor intuition without conceptions, can afford us a cognition.

Why we should believe professional cyclists

I renember a nice meeting in South Sardinia in 2002 (see my figure below) where a lot of famous people gathered for interesting talks in a wonderful surrounding.
A spin off from this Ogliastra Genetics Park – as the authors called it – is now a paper in PLOS Genetics that examines the heritability of 98 quantitative cardiovascular traits in 6,148 Sardinians.
Although the authors did not measure hematocrit, RBC related counts had an extremely high heritability (MCV 0.76, MCH 0.78). Hemoglobin was somewhat lower (0.47) which might in part be attributable due to some local selection factors. This result comes largely unexpected, as the high heritability of the MCV was not known so far.
In the absence of any assay for exogeneous EPO, hematocrit is used as an indirect parameter for testing athletes. I already wondered why cyclists are having such high values (if we exclude illegal drug use). This seems to be a genetically trait by self-selection – an anemic cyclist will not participate in the Tour de France. Yea, yea.

123-2325_img.JPG

Addendum

Here is an answer to the question what makes a champion ;-)

On the “Self”

If I would ever find the time, I would write a book on the “self”. Inspired by the Eccles/Popper book that I bought as a student, I always wondered how different the self is being defined in sociology, psychology/psychiatry, philosophy and theology.
As my current focus is more on genetics and immunology, I found a paper by Francisco Borrego on the “missing self” quite interesting as it highlights the genetic self is determined mainly by MHC class I molecules, where only NK cells transfected with H-2Dd were able to confer resistance for being self-attacked. It would be nice if other disciplines could also provide such simple answers, yea, yea.

Addendum

I have another suggestion: Zfp608 protects mouse mothers against immune-mediated attack by fetal cells.

Is there also a “digiself“?

Our identity has, for many years, existed quite independent of our physical incarnation in government, financial and other institutional databases. We are not real to the bank or other authorities unless we can produce something that links our physical self to our “real identity” in their database. We have many versions of this digital identity – or digiSelf, as I like to call it – spread among many databases, each with its unique characteristics, and inferred behaviours. Each one is more real to the institution – and ironically, to the people in that institution – than our physical self, what we consider to be our real self.

A simple POP answering machine

A script that I used for many years…

popreply.cfm

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<!--
CF_POPREPLY 1.02
Cold Fusion 3.0 POP mail answering machine
(c) 1 Dec 97 by Matthias Wjst (wjst@gsf.de)
bugfixes in 1.01 by 15 Jan 98
 * time stamp of sender may wrong, therefore only absolute time checking
 * reading blacklist now in loop
 * added to blacklist listproc
 * better email recognition
-->

<CFIF #ParameterExists(Attributes.LastInterval)#
  AND #ParameterExists(Attributes.LastUnit)#
  AND #ParameterExists(Attributes.PopServer)#
  AND #ParameterExists(Attributes.PopUser)#
  AND #ParameterExists(Attributes.PopUserPassword)#
  AND #ParameterExists(Attributes.WorkingDir)#
  AND #ParameterExists(Attributes.Replytext)#>

    <CFIF #Attributes.LastUnit# is "Day">
        <CFSET #unit#="D">
    <CFELSEIF #Attributes.LastUnit# is "Hour">
        <CFSET #unit#="H">
    <CFELSEIF #Attributes.LastUnit# is "Minute">
        <CFSET #unit#="N">
    <CFELSEIF #Attributes.LastUnit# is "Second">
        <CFSET #unit#="N">
    <CFELSE>
        error: correct time interval needed
    <CFABORT>
    </CFIF>
<CFELSE>
error: more parameters needed
<CFABORT>
</CFIF>

<CFFILE Action="WRITE"
File="#Attributes.WorkingDir#popreply.txt"
OUTPUT="#Attributes.Replytext#">

<CFIF #FileExists("#Attributes.WorkingDir#popreply.cmd")#>
    <CFFILE Action="DELETE"    File="#Attributes.WorkingDir#popreply.cmd">
</CFIF>

<CFPOP SERVER=#Attributes.PopServer#
    USERNAME=#Attributes.PopUser#
    PASSWORD=#Attributes.PopUserPassword#
    ACTION=GETALL
    NAME="Sample">

<CFIF #ParameterExists(ACT_MAILS)#>

    <CFLOOP QUERY="Sample">

        <CFX_POP3DATE DateMail=#Sample.date#>

        <CFIF #DateDiff(unit,DateMail,Now())# lt #(int(Attributes.LastInterval)#>

            <CFIF #FindNoCase("gateway",Sample.from,1)# is "0"
              AND #FindNoCase("dispatch",Sample.from,1)# is "0"
              AND #FindNoCase("prts",Sample.from,1)# is "0"
              AND #FindNoCase("notesys",Sample.from,1)# is "0"
              AND #FindNoCase("netlib",Sample.from,1)# is "0"
              AND #FindNoCase("MAILER-DAEMON",Sample.from,1)# is "0"
              AND #FindNoCase("root",Sample.from,1)# is "0"
              AND #FindNoCase("0000-Admin",Sample.from,1)# is "0"
              AND #FindNoCase("digi-info",Sample.from,1)# is "0"
              AND #FindNoCase("digi-request",Sample.from,1)# is "0"
              AND #FindNoCase("ftp-list",Sample.from,1)# is "0"
              AND #FindNoCase("ftp-mail",Sample.from,1)# is "0"
              AND #FindNoCase("ftpadmin",Sample.from,1)# is "0"
              AND #FindNoCase("ip-addr",Sample.from,1)# is "0"
              AND #FindNoCase("ip-oper",Sample.from,1)# is "0"
              AND #FindNoCase("listproc",Sample.from,1)# is "0"
              AND #FindNoCase("listserv",Sample.from,1)# is "0"
              AND #FindNoCase("mail-server",Sample.from,1)# is "0"
              AND #FindNoCase("daemon",Sample.from,1)# is "0"
              AND #FindNoCase("mirror",Sample.from,1)# is "0"
              AND #FindNoCase("netserv",Sample.from,1)# is "0"
              AND #FindNoCase("responder",Sample.from,1)# is "0"
              AND #FindNoCase("win-ip-admins",Sample.from,1)# is "0"
              AND #FindNoCase("mirror",Sample.from,1)# is "0">

                <CFSET Start = REFind("[-a-zA-Z0-9\._]+@([-a-zA-Z0-9_]+\.)+([a-zA-Z]{2,3})", from, 1)>
                <CFIF Start eq "0">
                    <CFSET Start = "1">
                </CFIF>
                <CFSET Stop = REFind("[^-a-zA-Z0-9@_\.]", from, Start)>
                <CFIF #Stop# is not "0">
                    <CFLOOP CONDITION="REFind('[A-Za-z]', Mid(from, Stop, 1)) GT 0">
                        <CFSET Stop = Stop - 1>
                    </CFLOOP>
                    <CFSET email= Mid(from, Start, Stop - Start)>
                <CFELSE>
                    <CFSET email= mid(from, Start, len(from))>
                </CFIF>

                <CFIF #FileExists("#Attributes.WorkingDir#popreply.black")#>
                    <CFFILE Action="READ"
                    File="#Attributes.WorkingDir#popreply.black"
                    Variable="blacklist">
                <CFELSE>
                    <CFSET #blacklist#="">
                </CFIF>

                <CFIF #FindNoCase(email,blacklist,1)# is "0">

                    <CFFILE Action="APPEND"
                    File="#Attributes.WorkingDir#popreply.black"
                    OUTPUT="#email#">

                    <CFFILE Action="APPEND"
                    File="#Attributes.WorkingDir#popreply.log"
                    OUTPUT="blat popreply.txt -t #email# -s #chr(34)#Re: #left(Sample.subject,19)##chr(34)#">
                </CFIF>

            </CFIF>
    
        </CFIF>
    </CFLOOP>

    <CFIF #FileExists("#Attributes.WorkingDir#popreply.cmd")#>
        <CFX_SHELLEXEC FILE="popreply.cmd" DIRECTORY="#Attributes.WorkingDir#">
    </CFIF>

</CFIF>

Genetics making up of Homo sapiens

Lets start a further workup of the evolutionary thread. With the complete human and chimp genome on our harddisks we are now able to compare genome sequence and genome activity of both species. A 2003 review by Sean Carroll summarizes our pre-genome knowledge about pan and homo lineages 6 Million years ago. The most interesting question is which mutations or genome rearrangements (Popesco 2006) are most relevant in the separation of lineages.

BTW I have still doubts about any positive effects of mutations (although this might be possible). Yes, I wonder also where are the exact pan-homo transitions (although the Sahelanthropus tchadensis might be a good candidate). Furthermore, I have doubts in survival of the fittest where non-survival of the non-fittest seem to be more relevant ;-) “Survival of the Sickest” is a CD of Mad Sin and a book of Sharon Moalem 2007.

Neuroanatomy might have provided some clues of a larger frontocortex in homo sapiens although the detailed cytoarchitecture could be as relevant. Noise of neutral substitutions could have confounded previous findings. It is also not clear to me if expansions and contractions of whole gene families are even more relevant. We may also renember that most quantitative traits have a polygenic background.

In any case FOXP2 could be associated with speech and language disorders (Vargha-Khadem 2005) where another prominent gene was now found in the 49 regions that are different between chimp and human but otherwise conserved (Pollard 2006). This new gene called “HAR1” is even expressed in the developing neocortex making it a prime candidate for species differentiation. Is there anybody able to convince me that the 18 fixed mutations in HAR1 have indeed a beneficial effect on brain development? A “leading edge” comment in Cell argues that all substitutions are upgrades from weak to strong base pairing:

Curiously, this weak-to-strong substitution bias in HAR1 extends over 1.2 kb, a region far larger than HAR1 itself. Such changes which also appear to characterize the HARs as a group undoubtely serve to strengthen RAN helices against dissociation…

I would also like to mention that male humans share more identity with male chimps than with female humans, at least on a genetic level, yea, yea.

Addendum

Even blogs have a half-life of less than 1 week. A new PNAS paper by Michael Oldham shows a more integrated view of human brain evolution by examining gene coexpression networks in human and chimpanzee brains. This seems to be another promising approach.