Prepared by daughter. Not to scale. Species not yet identified. Delicious.

EDIT: I got a couple of concerned emails. No, this did not happen to me. Yet.

Once I lived the life of a PI so rich,
Research was going along without a hitch.
Lab manager, four postdocs and grad students eight,
My lab took up the whole floor, and that felt great.

Five years later it all went to hell,
My renewal was declined, because no papers in Cell.
But I just read an RFA that is out,
I’m going to apply, and get it, without a doubt.

Nobody knows you,
when you lose your grant.
In your funding, not one penny,
and as for postdocs, I haven’t any.

If I ever get back on my feet again,
My department chair will not treat me with disdain.
It’s mighty strange, which is why I’m doing this rant,
Nobody knows you when you lose your grant.

Best version of the original, IMHO:

 

Dear  professor  Iddo Friedberg,

    

    First of all, I would like to introduce myself, my name is _____, 30 years old I  occupy a staff position of instructor at the department of pharmaceutical microbiology, faculty of pharmacy, ____ University, _____.

I was graduated in 2003 with an overall grade “excellence with honors” & I was the second among 1000 students.  I have a PhD scholarship totally funded by the ______ Ministry of High Education. The scholarship includes tuition fees, residence, health insurance and everything. Here is the link of the scholarships offered _________. I am interested in doing my PhD study in the field of molecular biology under your supervision. To fulfill the requirements of the scholarship, I should have a research proposal including the following items. I will apply to The University as soon as I receive the proposal.

 

The research proposal includes:

·                   Title Page (including Title, Keywords).

·                   Abstract

·                   General Overview of Research Area and Literature

·                   Key Research Questions and Objectives

·                   Methodology

·                   Tentative Timetable

·                   Selective Research Bibliography

 

I will be so grateful to you if you generously send me  a research proposal few days before the deadline(January 10, 2012)

 

 

N.B. other information is available in the attached C.V.

If you need any additional information or documents, please let me know

I am waiting for your reply as soon as possible in case of either acceptance or refusal.

Kind regards

g    Move pointer to the right.
e    Move pointer to the left.
n    Increment the cell at the pointer.
o    Decrement the cell at the pointer.
m    Jump forward past the matching i if the cell at the current pointer is zero.
i    Jump backward to the matching m unless the cell at the current pointer is zero.
c    Output the value of the cell at the pointer.
s    Input a byte and store it in the cell at the pointer.

As you can probably tell, I spent a lot of time working on genomics, but out pure generosity I am placing this incredibly useful language in the public domain. I’m sure we will see a BioGenomics group on Open Bioinformatics Forum any day now, and that genomics will prove to be a game-changer in the field of, um, genomics.

Allow me to end this post with the following inspirational statement:

nnnnnnnnnnmgnnngnnnnnngnnnnnnnngnnnnnnnnnngnnnnnnnnnnneeeeeoiggnnnnnnnn
nnnnncenncgggnnnnnnnncgncnnnnnnnceoooooooceeecgggnncoocgoooooooocncennn
nnnnncoooocennnnnnnnnnnnnnnnnnncggnnnnceeeencoooooooooooooooooooooooc

Thank you.

Brainfuck is a Turing-complete programming language consisting of eight commands, each of which is represented as a single character.

> Increment the pointer.
< Decrement the pointer.
+    Increment the cell at the pointer.
-    Decrement the cell at the pointer.
.    Output the ASCII value of the cell at the pointer.
,    Input a byte and store it in the cell at the pointer.
[    Jump forward past the matching ] if the cell at the current pointer is zero.
]    Jump backward to the matching [ unless the cell at the current pointer is zero.

Having arrived almost 3 hours early to JFK, flying back to Cincinnati, I spent the time coding up a Python script which inputs a string and outputs a Brainfuck source code which, when run with a Brainfuck interpreter, outputs said string. So for example:

to_brainfuck "Hello, World!"

Will output:

++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>++++++++
++++.>>+.+++++++..>+.<<<<++++++++++++++.------------.>>>>++++++++.----
----.+++.<.--------.<<<+.-----------------------.

The horror above is what Brainfuck source code looks like. When you run the above code with a Brainfuck interpreter, it will print "Hello, world!".

Brainfuck interpreters and compilers can be found here. Ubuntu has a Brainfuck interpreter called bf.

Probably not the best code I wrote, could use some honing. Still, it served the purpose of killing a couple of hours.

#!/usr/bin/env python
import sys

class bf:

    def __init__(self,format_bf=True):
        """
        Initiate brainfuck code string. Pointers are initiated to the
        following values, with their ascii equivalents shown
        ptr0 = 10 ptr0 is used as a loop counter
        ptr1 = 30
        ptr2 = 60  @
        ptr3 = 80  #P
        ptr4 = 100 #d
        ptr5 = 110 #n
        """
        self.bf_code = ''
        self.bf_code += "++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]"        

        # Index: cell number. Value: cell value.
        self.ptrs = {1: 30, 2: 60, 3: 80, 4: 100, 5:110}
        self.ptr_idx = 0 # which pointer is being used
        self.format_bf = format_bf # Format the bf code. Default True.

    def string_bf(self,instring):
        # Accepts a string. Outputs bf code which prints that string
        # when run with a bf interpreter
        for c in instring:
            self.bf_code += self.to_bf(c)
        # add a newline
        self.bf_code += self.to_bf(chr(10))
        if self.format_bf:
            self.bf_code = self._format_bf_code(self.bf_code)
        return self.bf_code

    def _format_bf_code(self,bf_code):
        # Format the bf source code to 70 chars / line
        outstr = ''
        for i,c in enumerate(bf_code):
            if i % 70 == 0 and i > 0:
                outstr += '%s\n' % c
            else:
                outstr += c
        return outstr

    def to_bf(self,c):
        # accept a character c, generate the bf code to print that
        # character.

        # increment / decrement the data pointer
        if c < '@':
            ptr_target = 1
        elif c >= '@' and c < 'P':
            ptr_target = 2
        elif c >= 'P' and c < 'd':
            ptr_target = 3
        elif c >= 'd' and c <'n':
            ptr_target = 4
        else:
            ptr_target = 5
        ptr_inc_str = self.increment_ptr(ptr_target)
        # Now increment / decrement the value which the pointer points
        ascii_target = ord(c)
        ascii_val = self.ptrs[self.ptr_idx]
        inc_val, inc_val_str = self.increment_val(ascii_val, ascii_target)
        self.ptrs[self.ptr_idx] += inc_val
        return ptr_inc_str+inc_val_str+'.'

    def increment_val(self,ascii_val, ascii_target):
        inc_val = ascii_target - ascii_val
        if inc_val < 0:
            inc_val_str = '-'*abs(inc_val)
        elif inc_val > 0:
            inc_val_str = '+'*abs(inc_val)
        else:
            inc_val_str = ''
        return inc_val, inc_val_str

    def increment_ptr(self,ptr_target):
        ptr_inc = ptr_target - self.ptr_idx
        if ptr_inc < 0:
            ptr_str = '<'*abs(ptr_inc)
        elif ptr_inc > 0:
            ptr_str = '>'*ptr_inc
        else:
            ptr_str = ''
        self.ptr_idx += ptr_inc
        return ptr_str

if __name__ == '__main__':
    my_bf = bf()
    if sys.argv[1] == '-f':
        intext = file(sys.argv[2]).read()
    else:
        intext = sys.argv[1]
    o = my_bf.string_bf(intext)
    sys.stdout.write("%s\n" % o)
    

To run:

chmod +x bf_string.py
./bf_string.py "Brainfork is awesome!" > mycode.bf # generate Brainfuck code into mycode.bf
bf mycode.bf # The brainfuck interpreter bf
Brainfork is awesome!

And mycode.bf will contain:

++++++++++[>+++>++++++>++++++++>++++++++++>+++++++++++<<<<<-]>>++++++.>
>>++++.<<+++++++++++++++++.>+++++.>----.<---.>+.+++.<+++++.<<<++.>>>--
.>+.<<<<.>>.>>++++.<----.>----.----.<++++++++.--------.<<<+.----------
-------------.

You can also run it with the -f option, where the input string will be read from a file.
 

UPDATE: and here is a brainfuck interpreter, written in Python.
UPDATE II: Following Vincent's comment, here is a fixed version of the interpreter. This time it should work with nested loops. Thanks Vincent.

#!/usr/bin/env python
import sys
class BfInterpreter:
    def __init__(self,inpath):
        self.iptr = 0
        self.cells =[0]
        self.cmdptr = 0
        self.infile = file(inpath)
        self.bfcode = self.infile.read()
        self.cloop_stack = [] # location of current startloop in bf code
        self.ploop_stack = [] # which ptr is current loopcounter
        self.loop_ended = False # Indicates if a loop counter just
                                # reached zero
    def inc_ptr(self):
        self.iptr += 1
        if self.iptr > len(self.cells) - 1:
            self.cells.append(0)
    def dec_ptr(self):
        self.iptr -= 1
        if self.iptr <= -1:
            raise ValueError,"negative pointer"
    def inc_cell(self):
        self.cells[self.iptr] += 1
    def dec_cell(self):
        self.cells[self.iptr] -= 1
        # Check if this is a loop counter
        if self.ploop_stack:
            if self.ploop_stack[-1] == self.iptr and \
               self.cells[self.iptr] == 0:
                self.loop_ended = True
    def start_loop(self):
        self.cloop_stack.append(self.cmdptr)
        self.ploop_stack.append(self.iptr)
    def end_loop(self):
        if self.cells[self.iptr] > 0:
            if not self.cloop_stack:
                raise ValueError,"no startloop character found"
            else:
                self.cmdptr = self.cloop_stack[-1]
        elif self.cells[self.iptr] == 0 and self.loop_ended:
            self.loop_ended = False
            self.cloop_stack.pop()
            self.ploop_stack.pop()

    def putc(self):
        sys.stdout.write("%s" % chr(self.cells[self.iptr]))
    def getc(self):
        self.cells[self.iptr] = ord(sys.stdin.read(1))
    def run_bf(self):
        self.cmdptr = -1
        while True:
            self.cmdptr += 1
            if self.cmdptr >= len(self.bfcode):
                break
            cmd = self.bfcode[self.cmdptr]
            # print cmd,
            if cmd == '>':
                self.inc_ptr()
            elif cmd == '<':
                self.dec_ptr()
            elif cmd == '+':
                self.inc_cell()
            elif cmd == '-':
                self.dec_cell()
            elif cmd == '[':
                self.start_loop()
            elif cmd == ']':
                self.end_loop()
            elif cmd == '.':
                self.putc()
            elif cmd == ',':
                self.getc()
if __name__ == '__main__':
    bf = BfInterpreter(sys.argv[1])
    bf.run_bf()

To run, download the file, name it (say, pybf) and then:

chmod +x pybf
./pybf bf_source_code_file.bf

And if that gave you a taste for the original, go here.

The IgNobel prizes are awarded annually for research that “makes you laugh, and then makes you think”. Actually, I liked their previous motto better: “research that cannot or should not be reproduced”. But like the Nobel prizes, IgNobels are not awarded only for science. For example, The mayor of Vilnius received the IgNobel Peace Prize for fulfilling every urban driver’s dream and running over an illegaly parked car with a BTR-60 (an armored personnel carrier mistakenly identified as “tank” by the IgNobel prize awarders, but what do these Harvard peaceneaks know about military stuff).

The Physiology Prize was given to Anna Wilkinson (of the UK), Natalie Sebanz (of THE NETHERLANDS, HUNGARY, and AUSTRIA), Isabella Mandl (of AUSTRIA) and Ludwig Huber (of AUSTRIA) for their study “No Evidence of Contagious Yawning in the Red-Footed Tortoise.”
REFERENCE: ‘No Evidence Of Contagious Yawning in the Red-Footed Tortoise Geochelone carbonaria,” Anna Wilkinson, Natalie Sebanz, Isabella Mandl, Ludwig Huber, Current Zoology, vol. 57, no. 4, 2011. pp. 477-84.

The prize I like best was the medicine prize awarded to : Mirjam Tuk (of THE NETHERLANDS and the UK), Debra Trampe (of THE NETHERLANDS) and Luk Warlop (of BELGIUM). and jointly to Matthew Lewis, Peter Snyder and Robert Feldman (of the USA), Robert Pietrzak, David Darby, and Paul Maruff (of AUSTRALIA) for demonstrating that people make better decisions about some kinds of things — but worse decisions about other kinds of things‚ when they have a strong urge to urinate.

In other entertaining, for want of a better term, the Wall Street Journal came out with an op-ed which made quite a few heads explode. Basically using a rather heavy-handed non-sequitur the author tried to unravel climate science:

The science [global warming] is not settled, not by a long shot. Last month, scientists at CERN, the prestigious high-energy physics lab in Switzerland, reported that neutrinos might—repeat, might—travel faster than the speed of light. If serious scientists can question Einstein’s theory of relativity, then there must be room for debate about the workings and complexities of the Earth’s atmosphere

For a full dissection of this weirdness, please go to Phil Plait’s response in Bad Astronomy.

 

For one, there is always room for questioning science. But that questioning must be done by science, using a scientific basis, and above all else be done above board and honestly. But that’s not how much of the climate science denial has been done. From witch hunts to the climategate manufactrovery, much of the attack on climate science has not been on the science itself, but on the people trying to study it. And when many of those attacks have at least a veneer of science, it’s found they are not showing us all the data, or are inconclusive but still getting spun as conclusive by climate change deniers. And if you point that out, the political attacks begin again (read the comments in that last link).

Second, the neutrino story has nothing to do with climate change at all. It’s a total 100% non sequitur, a don’t-look-behind-the-curtain tactic. Just because one aspect of science can be questioned — and I’m not even saying that, which I’ll get to in a sec — doesn’t mean anything about another field of science. Bryce might as well question the idea that gravity is holding us to the Earth’s surface.

The whole thing generated the delightful hashtag #WSJScience. Read the tweets before they expire.

Recently MIRA seemed to have developed a stochastic bug, one of those which are a serious headache to track down. Bastein called upon the MIRA community to help him. A couple of weeks ago, the “bug” was resolved to everyone relief. It was not a bug at all, but … well, I’ll let you read Bastien’s letter. Probably th funniest and geekiest error report I have seen since, well, ever. Reproduced here from the mira_talk email list with Bastien’s permission. WARNING: fairly geeky and fairly long. Not for everyone. But if you, like me, enjoy a good story travails of extreme bug hunting, I guarantee you will not be disappointed. (Because we have all been there, although personally I don’t recall encountering a problem that frustrating). Teaser: it was not a bug.

Dear all,

]]> http://bytesizebio.net/index.php/2011/09/02/5389/feed/ 0 http://bytesizebio.net/index.php/2011/07/07/john-smiths-genome-sequenced/ http://bytesizebio.net/index.php/2011/07/07/john-smiths-genome-sequenced/#comments Thu, 07 Jul 2011 16:35:08 +0000 Iddo http://bytesizebio.net/?p=5211 Springville University’s Genome Center in collaboration with Prof. I. M. A. Bigschotte from IvyLeague University have announced that the genome of Mr. John Smith from Centertown, USA has been sequenced and is now available online.

Dr. James Williams, director of the Center said: “We were running out of things to sequence, but I still had a budget to justify before the end of the fiscal year”.

“This project will give us insights into the 99% of the population we care nothing about, and frankly, I would not want to meet” says Prof. Bigschotte. “I don’t even know where Centertown is”.

“Johnny graduated from the local high school, and now working at the KFC”. Said Mr. Smith’s mother,  Mary, in whose basement Mr. Smith lives. “He cuts the grass and takes out the trash sometimes, but I really have to nag him to get to do something”.  ”I wish he will just move out” added Mrs. Smith.

Mr. Smith, who may or may not start classes at the local community college this fall, was unfazed by his recently found fame. “Like, I guess it’s nice to have all this stuff online, but, like, I couldn’t get it to fit on my Facebook wall”, said Mr. Smith, while digging into a party-size bag of Cheetos.

Iddo