Best Hegel Reference Heard Today, errr ever

as Hegel said… Kant’s requirement to become acquainted with the instrument, in this case the Mind, before one starts to use it, is like a resolution not to venture into water until one has learned to swim

The insight here is that its impossible to learn to swim without first getting wet.  A reference to this critique of Kant by Hegel was casually slipped into a discussion I had today with a friend about different approaches to introducing new technologies into society. (The quote above came this blog, who also cites the original passage.)

Video: Virtual Genomic Counseling vs. Face-to-Face

The PBS television station KQED in San Francisco recently aired a very thoughtful segment comparing online genomic counseling through DNA Direct to traditional face-to-face counseling via UCSF.  Check it out:


KQED, Genetic Testing through the Web. Feb 20, 2007.
Full discolure: I am employed by DNA Direct.

Ispecies Mash-up

Harbinger!  I-species is a mash-up of a variety of information sources…

Human
Golden Eagle
Morel (Morchella esculenta)
Helicobacter Pylori
Toxoplasma gondii (see this post at The Loom)

Check it out!  See also the I-Species Blog

Hat tip Open Access News with this post…snip: “Once scientists see the value of freeing-up data, mashups will explode…”

Want more mash-ups?  Look no further

What consequence human health?


454 wins gold in WSJ Tech Innovation Awards

454’s sequencing technology was awarded the gold prize in this years WSJ Innovation Awards.  The money quote:

"Judges saw the [sequencing] technology as ‘potentially’ or ‘clearly’ revolutionary"

Michael Totty. "Innovation Awards: A Better Idea" WSJ October 24, 2005.  (Or listen to a podcast)

Leroy Hood on the Future

Leroy Hood, tireless generator of good quotes (among other things):

My prediction is that within 10 years, we will have a predictive medicine that will have two separate components.

No. 1, it will have the ability to sequence every human’s genome for
less than $1,000. We will be able to make predictive health histories for each individual from the varying genes that come from that
sequencing.

Perhaps a better term than predictive health histories is
health futures.  Is it me, or does having health sandwiched between predictive and history feel claustrophobic?

No. 2, we will have a little hand-held nanotechnology device that
will prick your finger and make a thousand measurements and by
wireless, send that to a server. It will analyze all your past records.

It will say, "Nothing’s changed. You’re fine. Do it again in six
months." Or it will say, "Go see your oncologist or go see your
rheumatologist" or whoever might be appropriate.  Your physician would get an e-mail, too.

There’s more from Leroy:

Take into account that your genome and mine differ by 6 million
nucleotides…

We have to treat you differently than we treat me and everybody
else. How we create an era of highly personalized medicine will depend
entirely on new diagnostic, therapeutic and ultimately, these
preventive techniques.

What we’ll do is feed your genome sequence into a grid network of
computers that will do many different kinds of analyses simultaneously.
You’ll get a summary sheet that says here are the things and here are
the probabilities that you’ll likely have to worry about in the future…

Oh yeah, and this is good too..

It takes five years for people to get anything. The first few times
they hear it, they can think of a thousand reasons why it’s wrong.
Then, after they’ve heard it a few more times, it starts to sound more
logical.

If you’re a missionary, you’ve got to be patient with your
congregation. We are at the very beginning stages of thinking about
this.

Read the whole piece in the SeattlePI.

Helicos shoots for $5K genome

Helicos Biosciences is featured in this month’s MIT Technology Review.  Helicos is developing sequencing technology based on the work of Stephen Quake.  The article provides a description of how their sequence-by-synthesis method works:

Helicos’s technology eliminates many of the expensive and
time-­consuming steps that are central to conventional DNA sequencing.
The machine works, in essence, by photographing the process of DNA
replication.

Technicians chop up the DNA to be sequenced into
short pieces just a few hundred letters long and split each piece into
single strands, which will serve as templates for new DNA copies. They
take about 1.2 billion of those templates and chemically anchor them
side by side, like tiny bristles, on a glass slide. The Helicos machine
then washes the slide with DNA-synthesizing enzymes and fluo­rescently
tagged versions of the DNA bases—the molecular building blocks
represented by the familiar DNA letters. It introduces copies of just
one base at a time; wherever a template strand calls for that letter in
the next open position, the enzymes incorporate it into the growing DNA
copy. The machine then washes out the extra, unincorporated bases and
takes a picture that reveals the newly incorporated bases as dots of
lights. Once it has captured an image, the device pumps in chemicals
that stop the new bases from glowing, in preparation for another cycle
of washes and photos.  The Helicos machine repeats the whole
process over and over, building up the new DNA copies one letter at a
time. A computer analyzes all the captured images to determine the
sequence of each short strand; then, using the published human genome
sequence as a guide, it pieces all the short sequences together into a
single complete one.

The Helicos sequencing machines are expected to be commercially available by late 2006 or early 2007.   How will the cost of sequencing a human genome on one of these machines compare to today’s standard?

Today:

"using about 100 state-of-the-art sequencing machines to fully sequence
the 3.2 billion DNA letters that make up one person’s genome would take
six months and cost $20 million to $30 million."

2006-2007

"When Helicos’s commercial machine is released,
says Lapidus, it will sequence a whole genome start to finish in three
days and for a cost of $5,000."


Corie Lok. "Deciphering DNA, Top Speed" MIT Tech Review. May 2005.

Stephen Quake Lab.

Helicos Biosciences

See also: Biotage’s Pyrosequencing (sequence-by-synthesis) tutorial …with video

Population Genetics Technologies

Information is scant otherwise, so here is a snip from the press release:

Dr Sydney Brenner, has devised a new method for obtaining sequence information from thousands of genomes simultaneously…This method, to be developed by a new company called Population
Genetics Technologies, is expected to reduce significantly the cost of
studying large populations of genomes…The Intellectual Property and related patent applications underlying
the technology were licensed from Compass Genetics LLC, a partnership
formed several years ago by Drs Sydney Brenner, Sam Eletr and Philip
Goelet.

Dr Sam Eletr…“our new method, if successful…is expected to provide a significant cost advantage over other techniques which analyse one genome at a time…because our method will allow the mixing of thousands of samples in one test tube and the simultaneous interrogation of all of them in one experiment, instead of in as many experiments as there are genomes in a population.  Although pooling techniques that allow simultaneous analysis of multiple genomes have been used, these only provide population-wide characteristics, such as the frequency of gene variation, and not information specific to individual genomes. We expect our technology to allow handling much larger numbers of genomes than pooling does and to have the further advantage of protecting the identities of individuals involved in any population study by allocating them a code that may be kept confidential. We expect it also be applicable to any collection of DNA molecules and genomes, whether from plants, animals, micro-organisms or humans.”

Resources:
Syndey Brenner bio.

Press release. "Mass Analysis of DNA from Whole Populations." 4/20/05.

Development of Sequencing Technology

Two grafs on the development of sequencing technology from a recent article in Bioscience Technology.

1) Sequencing technology is "frozen in time", still searching for a breakthrough:

Progress in gene sequencing has arisen more from improved methods than
ground-breaking instrumentation. Glenn Schulman, PharmD, marketing
manager at 454 Life Sciences (New Haven, CT) points out that gene
sequencing technology has become frozen in time circa 2000. “Things
pretty much stopped with capillary electrophoresis-based
instrumentation,” he says. “There have been incremental improvements,
but nothing truly enabling.”

2) Logarithmic Scaling of 454’s sequencing-by-synthesis technology (see image)

454’s progress has been phenomenal since it reported its first results,
on about 25 base pairs, in late 2001. Since then scale-up has been
logarithmic: 33 kbp in 2002, 2.8 Mbp in 2003, and about 20 million bp
today (about the size of a bacterial genome) in a 4.5 hour run. Dr.
Schulman sees no end in sight to Moore’s Law-type scaling, which could
result in sequencing a whole human genome — 30 Gbp — in a matter of
days or hours.

Resources:
Angelo DePalma. "Sequencing in the post-genomic age." Bioscience Technology.

Biotage’s Pyrosequencing (sequence-by-synthesis) tutorial …with video

Solexa Developments

Solexa and Lynx Therapeutics have completed their merger.  Solexa is now up and running on the NASDAQ with the ticker SLXA.  They are developing technology that promises to bring down the cost of sequencing.  They recently completed their first full genome sequencing job using their new "DNA cluster" technology.