In the traditional model of computing, programmers write their codes in C or other high-level
(i.e. human-readable) languages. Then a compiler (e.g. gcc) converts that code into assembly
and machine (byte) instructions. This is because the microprocessor can understand only 0s and 1s,
whereas the humans tend go crazy trying to make sense of such code. The assembly language is a
happy compromise between the two. It presents the machine or byte-instructions in human-readable
Yesterday, I attended an interesting talk by Ian
Derrington, who is currently working as a post-doctoral researcher
in the lab of professor Jens Gundlach
at the University of Washington (UW). For those who do not know, Gundlach lab
is the first to identify and use MspA as an efficient pore molecule for
nanopore sequencing, and they published several key papers related to
development of the technology over the years. In my understanding, Illumina’s
licensing of MspA-related patents from UW is the basis of their IP lawsuit
against Oxford Nanopore.
In a remarkable feat, Professor Rene Anand of Ohio State
University, one of our collaborators from the
electric eel genome project, grew near complete human brain organoids on a
petri dish in his lab. Here is how the method works. He starts from the skin
cells of a person (could be you) and reprograms them into induced pluripotent
stem cells (iPSCs) using Yamanaka’s method. Then he grows those stem cells
into neural organoid, and you can see your ‘baby brain’ sitting in a test
tube. It is truly your brain, because it has the identical genome as yours.
Linkage and association studies have mapped thousands of genomic regions that
contribute to phenotypic variation, but narrowing these regions to the
underlying causal genes and variants has proven much more challenging.
Resolution of genetic mapping is limited by the recombination rate. We
developed a method that uses CRISPR to build mapping panels with targeted
recombination events. We tested the method by generating a panel with
recombination events spaced along a yeast chromosome arm, mapping trait
variation, and then targeting a high density of recombination events to the
region of interest. Using this approach, we fine-mapped manganese sensitivity
to a single polymorphism in the transporter Pmr1. Targeting recombination
events to regions of interest allows us to rapidly and systematically identify
causal variants underlying trait differences.
Between 2000-2005, computer company SUN Microsystems developed a number of
major improvements (zones, ZFS, dtrace) to Solaris, which was their version of
the unix operating system. Then in 2005, SUN released all Solaris code
publicly through a CDDL license along with 1600 patents. The CDDL license was
GPL incompatible, and therefore linux authors could not copy Solaris code and
claim as their own.
By mid-90s, software companies started to think about ways to make sure
millions of would be internet-connected devices talk to each other. XML, a
generalized version of highly popular HTML, was one possible option. In fact,
for many years it was the only option. XML standards were designed in mid-90s
by a committee of eleven well-respected programmers and had widespread backing
Yesterday I attended a seminar on Apache Spark,
and thought the readers may find this new technology interesting for their
programming and data analysis. There is no bioinformatics connection at the
moment, and I am simply mentioning it as a type of fault-tolerant software-
hardware technology with a lot of development work going on, and may turn out
to be useful in the future.
Readers wanted us to comment on the ongoing dogfight related to CRISPR
patents. Only thing we can say is that patents related to publicly funded
research should be placed in the public domain, because otherwise the patent
fight damages basic research at several levels.
Eric Lander wrote an excellent
article reviewing the
history of CRISPR. It is well-written and covers fascinating stories about the
early scientific work of some of the key players. A take-home message is that
unusual discoveries in basic science do not start from the heavily funded
famous labs. Kudos to Lander for recognizing the roles of young, unknown and
risk-taking scientists in pursuing such discoveries.