With this variation on a famous statement by the philosopher Descartes,
I would like to express that writing about what happens in my life
is important to me.
Today, I received an email from Sarah Ng with respect to the two discrepancies that I had
found last weekend in the
Supplementary Table 3 of the Exome sequencing identifies MLL2 mutations as a cause of Kabuki
syndrome paper. She explained that for kindred 25
the DNA mutation should have been "c.A13579T" (instead of "c.A13580T"),
which indeed results in "p.K4527X" as mentioned in the column "Predicted
Amino Acid Change". And with respect to kindred 50, she agreed that
there was a typo in the protein position and that it should have
read "p.P443HfsX487" (instead of "p.P442HfsX487"). I am totally
satisfied with the answer. I have update my MLL2
page accordingly. She thanked me for checking their results, but
it was only because I tried to understand the data (in order to use it
for web page), that I found these small discrepancies. I consider them
small, because from my own experience as a software engineer, I know
that these type errors are very easily made. And of course, they do
in no way diminish the discoveries as presented in the paper. Actually,
I should thank her for her contribution to finding the cause of
Kabuki Syndrome. Although the discovery will have no direct effect for
children who are affected by this mutation, it will benefit many
parents in future to get a clear diagnoses. Andy, our son, who did receive a clinical diagnoses of Kabuki
Syndrome, will also be tested for a defect in the MLL2 gene in the
coming months and we will know whether he has the defect or not.
I expect more discoveries to be made in the coming years.
The first case is in kindred 25 for mutation "c.A13580T",
which represents a change of an A into a T at location 13580
of the DNA sequence. According to the data given at
Homo sapiens myeloid/lymphoid or mixed-lineage leukemia 2
(MLL2), mRNA, the base pairs for the protein at location
4527 is "AAG", which encodes for lysine (K). The given
predicted amino acid change for this kindred is "p.K4527X".
However, for the given mutation the "AAG" sequences is
changed into "ATG", which encodes for asparagine (M) according
to the Standard Code, and not for a stop sequence, as represented
by the "X". It seems that the predicted amino acid change
should have been "p.K4527M". Note that if the mutation would
have occured at location 13579, the sequence "AAG" would have
been changed into "TAG", which indeed is a stop sequence.
Also in case the sequence would have been "AAA", the only
other sequence that encodes for lysine, a mutation at location
13580 would also not have given a stop sequence, because "ATA"
encodes for isoleucine (I).
The second case is in kindred 50 for mutation "c.1324delC",
which stands for a deletion of an C at location 1324. At that
location there starts a sequence of five C's. So, actually,
the delection could also have been in one of the next four
locations. The given predicted amino acid change for this
kindred is "p.P442HfsX487". And although the matching sequence
"CCC" for location 442 in the protein does encode for proline
(P) it does not change with the deletion of an C at location
1324. However, the sequence "CCA" for location 443 does
change into "CAC", which encodes for histidine (H). It seems
that the prediced amino acid change should have started with
"p.P443HfsX".
I have tried to contact the authors and informed them about
my findings.
Today, we had some heavy rain. We got about one month
of rain in half a day. This resulted in some flooding.
The picture on the right shows a waterfall in a tunnel
that I usually take. In some part of the trip, I had to
use the pavement and at some places even the pavement
was flooded. This KML files,
which can be viewed with Google Earth, shows the route I took biking to and
from my office including some areas in which some
flooding occured.
This morning at 11:42:11, I bought Opperlandse taal- & letterkunde by Battus from bookshop De Slegte for € 7.50. This is about a variant of
the Dutch language called Upperlandic, which is a wordplay on Netherlandic,
which is the literal translation of Nederlands, the Dutch name for Dutch.
I looked into the issue with respect to the Knot Nonogram not being solved, while classified as line solvable.
I have discovered that there is a serious problem with my line reasoning
routine in the Nonogram solver I used last Sunday.
I have not figure out whether this has been a case that never has been
handled correctly, other whether it concerns a bug that has been introduced
in the process of improving the routine. I am quite sure that there is
nothing wrong with the definition of line solvable of Jan Wolter and the classification of the Knot Nonogram as being
line solvable.
Yesterday, the long awaited press
release, Discovered gene
causes Kabuki syndrome, came about the likely cause of Kabuki Syndrome, the syndrome Andy has
been diagnosed with. Multible defects where found in the MLL2
gene which encodes the MLL2 enzyme. Because
with Kabuki Syndrome there is a rather large variability of medical
issues, it is interesting to see if there is a correlation between
the various defects that where found and the various medical issues.
This is definitely a very interesting find.
Last week, I exchanged some emails with Jan Wolter about his survey of Paint-by-Number Puzzle Solvers and my Nonogram solver. (Nonogram is one of the alternative names
for Paint-by-Number Puzzles.) He tested the version that I published
on August 23, 2009, which is a
rather experimental version. He mentioned that it could not solve
the Knot puzzle,
which according to him is line solvable. I was a little surprised by
this. I did run the version of the Nonogram solver and discovered that
it did solve this puzzle, but also that it this is not immediately
clear from the output generated by the program. I also discovered
that there is a bug in the printing routine of the program. This
program starts with a simple line solver, which did not solve the
puzzle. Either this simple line solver is too simple (or has a bug)
or his definition of line solvable is different from what I have
in mind, which is solvable with repeatedly applied line (row or column)
reasoning. I also tested the version of the Nonogram solver (not
published) which I wrote for trying to solve his set of 5000 two-color, 30 by 30 puzzles. This solver too
did not solve this puzzle. These finding have aroused my interest
in Nonogram solvers again, and also made me think about a new
implementation. I have informed Jan about my finding, so it is possible
that he might update his entry about my solver.
This afternoon, Li-Xia and I went
into the city for some shoppings. We visited Photo galery "Objecktief" where we look at the photographs,
the prints, of Thea Hillen.
She uses a special technique where she prints two, or sometimes even
three, negatives on top of eachother. We also went to the bookshop of De Bijenkorf. Here I found a book with all the
paintings and sculptures of Jan Wolkers. I was happily surprised when I saw that the price
of the book had dropped from € 37,95 to € 12,50.
At 14:47:20, I bought the book Jan Wolkers: Schilderijen, tekeningen,
beelden (ISBN:789040096570), which is published by Waanders. At home, I discover that the books has been sold out
for some time.
Yesterday evening, I connected the old harddisk to johan (replacing the DVD drive) and when I started
the computer, it performed a CHKDSK on the drive and made some
repairs. After this, I could simply access the drive. Next I
tried to boot from this drive, and that too worked without
problems. This morning, I swapped the new drive with the old
drive and connected the DVD drive again. The computer is still
working as before. I think, I keep the new drive, because I am
not completely sure that the old drive will continue working
without problems. I also have decided to make daily backups to
Freecom mobile hard drive
of my emails.
This afternoon, Andy and I went to
Mediamarkt to have the technical service have a look at
our computer johan.
They too concluded that the harddisk had failed. I went into
the shop and at 16:39:32, I bought a new 320GB harddisk, a Samsung
HD322HJ with serialnumber S17AJ90Z441680 for € 59,99.
It was the cheapest internal harddisk they were selling, as far
as I could see.
After dinner, I installed it in johan after I blew
the dust out of the inside and removed the Samsung HD321KJ
with serialnumber SOMQJ1KP710274. I just the recovery disk
to format the drive and install Windows XP. Next I used the
ASUS DVD to install some drivers for the intergrated sound
and network devices on the motherboard. Finally, I downloaded
Firefox and allowed Andy, who had been watching the whole
formatting and installation process with much anticipation,
to surf the internet for some time before I brought him to bed.
I guess, I will need the coming days to install some more
drivers and software. I am also trying to find another Samsung
HD321KJ drive in an attempt to revive the harddisk by swapping
controllers. But maybe I will first try to simply hook the
drive as a second drive to see if I can access it that way,
because from what I read on the internet, the message "Disk read
error" can also mean that the Master Boot Sector is corrupted
or that there is a bad sector in one of the files that are read
during the booting process.
This morning, I got a disk reading error during the booting of
our computer named johan.
It seems that the hard disk had died, or at least the controller.
I played a little with the cables and the connectors, but that did
not fix the problem. I think I am going to bring the computer to
Mediamarkt, where I bought it three years ago, to see if I can get
it fixed.
This evening, I finished reading
the book Meta Maths: The Quest for Omega by
Gregory
Chaitin. I started reading this book on July 31, the day I bought the book from bookshop De Slegte for €9.95. I am not very impressed
by this book. I think that the publisher should have done
some more editing, because this book is not very well written.
It looks like the author did not really have a clear goal in
mind. There are two appendices of 13 and 31 pages which seems
to tell the same story as the main text, but from a slightly
different perspective. I am also dissapointed by the lack of
mathematics in the book and the intuitive approach that the
author takes. At some places Chaitin also sounds quite arrogant,
like he made some very shocking mathematicals discoveries, while
the book fails to explain these discoveries in a convincing
manner. I think that Hofstadter did a much beter job in his
Gödel, Escher, Bach.
On page 148, in the section "On Creativity" the author makes
mention of "metamath" and I wonderd if he was refering to
the Metamath
proof checker.
This afternoon, I phoned with Bert
to ask if we could visit them to look at their holiday pictures
and show our pictures from China.
He said that they wanted to go to the movie Inception.
After some considerations, we decided to join them. The automatic
reservations system reported some error, but when we arrived about
half an hour ahead, there where still enough seats. I found
Inception an interesting
movie, but whether it really deserved a 9.2 as given on IMDB,
I doubt. I do not understand why they needed three levels of
dreaming for the inception. Also, the student Ariadne, although
just hired by Cobb, the expert, soon displays a level of understanding
of this type of dreaming that seems far beyond her experience.
I even expected the movie to end with a scene where Cobb wakes-up
from a dream with her sitting besides him explaining that the
dream was needed to help him overcome the death of his wife. But
that did not happen. I found the ending of the movie quite strong.
This morning, it was the first time that I went to bookshop De Slegte. First, I looked among the new books
downstairs. Next, I went upstairs to look at the newly arrived
second hand books. When I skimmed throught them, I came across
Meta Maths: The Quest for Omega
by Gregory Chaitin. At 11:44:03, I bought the book for € 9.95.
In the afternoon, I started reading
the book.
Today, I finished readingDertien
(meaning thirteen), the Dutch translation of Black Swam Green
by David Mitchell, which I started reading last Monday. I bought
the book on Saturday, March 13, 2010 at
14:04:23 as one of three books for five Euro from bookshop De Slegte. The book is about the thirteen
year old Jason. The first part of the book I found a little
hard to get throught, maybe also because some chapters
end very abruptly, like some part of the story was accidently
left out. But about half way, I really started to enjoy this
book. I think at some place Jason is too smart for his age,
while at other places being to naief. Every chapter is almost
a story on its own. I felt that some chapters had a little too
much coincidential events to be realistic. What I did like is
that the book is set in 1982 and contains many references to
events and items of that time, which brought back many sweet
memories from my own youth. Everything together, I think this
quite an enjoyable book to read.
Around 11:54, Li-Xia and I made
a walk in the neighbourhood, I also took some pictures of
the Xinhua International City of Books.
(One of the pictures.)
Around 12:20 we went into the bookshop and looked around a little.
Finally, I decided to buy three Go books,
which cost 114¥ together. One of the books contains the games
of a famous Chinese Go player (ISBN:9787807059905) and costed 66¥.
The other two books contain Go exercises (ISBN:9787811001112 and 9787811001129)
and costed 24¥ each. According to the ticket, I bought the books
at 13:08:32. We left for home at 13:11.
This afternoon, Li-Xia and I went
to the Xinhua International
City of Books. We arrive at 18:46 and looked around,
but I was not really in the mood for buying books. Part three
of Knuth's The Art of Computer Programming was sold,
and I did not feel that part two was interesting enough.
I did have a look at the Go books, but again, non of the
books felt interesting enough to buy.
At 19:52:29, I bought two Chinese Tin Tin albums printed
by China Children's Press
& Publication Group about the trip to the moon
(ISBN:9787500794479 and 9787500794486) for 12¥ each,
and also a Megaminx, regular dodecahedron 'Rubic' cube,
made by China Qun Jia
for 38¥. At 19:59:16, I bought a new edition of the
famous Red Book with the statements of Mao
(ISBN:9787010083117) for 30¥ just before we left the
shop.
This evening, I finished reading
the book Vita, the biography of Vita Sackville-West
written by Victoria Glendinning. I read the first chapter
on the night of February 10 of this year, when I could not
fall asleep. Then I continued reading the book this holiday
in China. I bought the book on Saturday, October 18, 2008, mainly because I needed
a fourth book for a four for 10 Euro deal and because it
was a biography. While reading the book, I discovered it
was again a book about an artist, a writter, with an
abnormal style. Although she was happily married with
her husband and they clearly loved eachother very deeply,
they both had homosexual relationships with others, she
more than her husband. Nevertheless, I found it an interesting
book to read. The book is well written and reads with
ease.
This morning, Li-Xia, Xiao-Zhong
(her brother), and I went to the historical museum here in Urumqi.
There I accidently met with Alan Libert from the University of Newcastle in Australia.
He is a lingust studying, beside other things, Turkish languages.
I always had thought that Uyghur and Turkish were like dialect
of the same language, but he told me that he thought that they
where further apart, and that speakers of both languages could
probably not understand each other. He had visited the Netherlands,
the universities at Groningen and Leiden. He also knew Afrikaans
and thus understood Dutch a little. When we left, he said: "Totzien",
which is Dutch for "see you". It was nice meeting him.
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