Monday, October 27, 2008

The DNA Network

The DNA Network

Cramps and groans? Consider Crohn’s [The Navigator - Navigenics Blog]

Posted: 27 Oct 2008 09:37 PM CDT

Michael Nierenberg, M.D.

imageCrohn’s disease isn't something that usually comes up in cocktail party conversations.  It isn't featured prominently in television shows or radio spots. Ask your average person what Crohn's is, and they likely will be hard-pressed to give you the right answer.

But this chronic inflammatory bowel disease is featured on the Web site of the New York Times, putting a face – or faces, in this case – to this rarely discussed disorder. In this interactive feature, seven people ranging in age from 19 to 61 share their experiences with the condition that has been diagnosed in more than 300,000 Americans.

"It takes forever to get diagnosed with Crohn's," recounts Ryan Walsh Horowitz, 19, of Brooklyn. "They thought I was anemic. They thought I had leukemia – and a bunch of other things."

That is not surprising, nor an isolated problem.

Crohn's has long been overlooked or misdiagnosed in the general public. The most common symptoms are, well, common: diarrhea, constipation, gas, abdominal pain, bloating and loss of weight. So it's easy to see why many other health conditions are often suspected first.

Hitch-slapped []

Posted: 27 Oct 2008 07:35 PM CDT

drosophila.jpg crosby.jpg

I don’t always agree with Christopher Hitchens, but this paragraph made my heart flutter for its celebration of two things I love: genetics and Pittsburgh, PA.

It was in 1933 that Thomas Hunt Morgan won a Nobel Prize for showing that genes are passed on by way of chromosomes. The experimental creature that he employed in the making of this great discovery was the Drosophila melanogaster, or fruit fly. Scientists of various sorts continue to find it a very useful resource, since it can be easily and plentifully “cultured” in a laboratory, has a very short generation time, and displays a great variety of mutation. This makes it useful in studying disease, and since Gov. Palin was in Pittsburgh to talk about her signature “issue” of disability and special needs, she might even have had some researcher tell her that there is a Drosophila-based center for research into autism at the University of North Carolina. The fruit fly can also be a menace to American agriculture, so any financing of research into its habits and mutations is money well-spent. It’s especially ridiculous and unfortunate that the governor chose to make such a fool of herself in Pittsburgh, a great city that remade itself after the decline of coal and steel into a center of high-tech medical research.

Another Consideration For Genetic Sequencing and Privacy [The Genetic Genealogist]

Posted: 27 Oct 2008 02:17 PM CDT

James Watson (February, 2003)

(Jim Watson via Wikipedia)

As if there wasn’t enough to worry about during the genetic revolution, researchers have found a way to characterize redacted genetic sequences from whole-genome or large-scale sequencing.

Here’s how it works.  Let’s say that Mr. X has had his genome sequenced, but doesn’t want to know the results of some genes known to influence the development or progression of Alzheimer’s Disease.  So when he receives his genomic sequencing, these genes have been ‘redacted’, or removed from the data.  This is exactly what James Watson decided to do when he received his data.

Characterizing Redacted Genes

However, researchers have characterized one of Watson’s redacted genes by examining the sequences surrounding the gene in question.  Often, when we inherit a gene from our patents, we receive that gene as well as some of the surrounding genetic sequence.  By examining the surrounding sequence, some insight into the redacted gene is gained.  For example, if I gave you the quote “A penny _____ is a penny earned”, you can derive from the surrounding words that the missing word is “saved.”

From an article discussing the researcher’s work:

“When the researchers told Watson about the paper’s results prior to publication, he redacted an additional 2 million DNA letters surrounding his APOE gene. This will make determining his redacted sequences much more difficult to decode - but not impossible, the authors write.”

Ethical Concerns

This ability, of course, raises numerous ethical concerns.  If we value the protection of privacy, even for people who make part of their genetic sequence available online, how do we protect their privacy?  Asking people to avoid this type of analysis won’t work, of course.  Is the only answer to redact huge portions of DNA surrounding redacted genes?  Or are we faced with an all-or-nothing question: either people put their entire sequence online (or just portions but face the risk of this analysis) or they keep their sequence private?

The authors of the study are also concerned about the potential problems.  From the paper:

“We believe the potential for such indirect estimation of genetic risk has considerable relevance to concerns about privacy, confidentiality, discriminatory and defamatory use of genetic data, and the complexities of informed consent for both research participants and their close genetic relatives in the era of personalized genomics.”

For more discussion, see the always-great Genetic Future.  See also “DNA detectives can decode ‘censored’ genomes” in New Scientist.

The article: Dale R Nyholt, Chang-En Yu, Peter M Visscher (2008). On Jim Watson’s APOE Status: Genetic Information is Hard to Hide. European J. of Human Genetics (DOI: 10.1038/ejhg.2008.198).

The Battle Against Breast Cancer Gets Personalized [deCODE You]

Posted: 27 Oct 2008 12:35 PM CDT

deCODE Breast Cancer enables women to understand whether they may benefit from more intensive screening, monitoring or preventive drug therapy.

A new genetic test assessing a woman's risk of developing the most common forms of breast cancer has arrived. Can the test, developed by the biopharmaceutical company deCODE, improve the way doctors screen for breast cancer?

Breast cancer kills 40,000 people a year in the U.S. This is about the population of Atlantic City, New Jersey. Imagine, each year an entire city wiped out by breast cancer.

To help fight breast cancer, a new test assessing individual risk has just become available. For women without a clear family history of the disease, the deCODE BreastCancerTM test assesses their personal risk of developing the most common forms of breast cancer. The DNA test, launched by the biopharmaceutical company deCODE, makes it possible to identify those women at significantly higher than average risk, helping doctors use new screening technologies and treatments in a more targeted, personalized and effective manner.

The key to fighting breast cancer, like all cancers, is early detection, which is why the medical field is buzzing over deCODE’s new breast cancer test.

“This test helps define individual prevention which is what so many of my patients want,” says Owen Winsett, MD, founder and director of the Breast Center of Austin.

Dr. Winsett, who has already ordered the test for 25 of his patients, can’t hide his enthusiasm over how the decode breast cancer test is changing the way he screens for the disease.
“I’m excited to be able to extend my screening and prevention practice. I plan to make this test a standard tool for helping me decide which of my patients may benefit from screening at an earlier age, or benefit from more intensive screening, including breast MRI’s. And then if my patients don’t have breast cancer, to motivate them to begin healthy preventive strategies.”

The test is not offered directly to individual women, but rather ordered by doctors on the request of their patients. deCODE advises that the test-which scans a woman’s genome for seven widely replicated single-letter variations (SNPs) in the human genome that are linked to increased risk of breast cancer-is a way to better connect doctor and patient.

Dr. Winsett agrees. He recommends that before taking this test women should consult their general practitioner, and if their doctor is uncertain about how to use the results of the test, to seek out a breast cancer specialist.

Like all new technologies - particularly those that may change accepted clinical practice - this type of risk screening has raised concerns in some quarters. Some critics have argued that the test is not accurate enough because it’s not based on a large enough sample of women to predict risk of breast cancer. However, the evidence tells a different story. According to Dr. Winsett, epidemiological studies on breast cancer present a fairly straightforward argument that deCODE’s genetic test does indeed give a picture of a patient’s baseline risk. The evidence shows that the seven SNPs in the human genome that the decode test scans for are linked to an estimated 60 percent of all breast cancer cases. These findings are derived from integrated data from discovery and replication studies published in major peer-reviewed journals and involving nearly 100,000 breast cancer patients.

“I remind patients this test is one peice of the puzzle,” says Dr. Winsett. “The test won’t tell patients if they will get breast cancer or if they won’t. It shows the average risk, and then says where a woman stands in relation to that average and then what her absolute risk is. As a doctor, deCODE’s breast cancer test helps me evaluate a patient and make a future plan for prevention and testing.”

Still, some non-clinicians feel genetic testing only benefits women who have a strong family history of breast cancer. One bioethicist recently wrote on an MSNBC blog that “the tests Decode and other companies are offering are more likely to empty family pocketbooks and leave women with a false sense of security than they are to prevent breast cancer.”

Dr. Winsett finds this argument muddled. There are already tests to pick up genetic risk factors for highly familial forms of the disease, and neither those tests nor deCODE’s for measuring risk will cure or prevent breast cancer. Dr. Winsett notes that mammograms, ultrasounds and breast MRIs don’t prevent women from getting breast cancer either, but doctors still use them because they are tools to help detect breast cancer.

“Sometimes a patient will say, 'I’ve had a mammogram regularly, so how can I get breast cancer?’ It’s easy to think that. But neither mammograms nor the deCODE test can on their own prevent breast cancer. It’s how you use the information from the genetic test to shape a patient’s care that leads to prevention or early detection.”

Genetic risk screening for breast cancer might sound like cutting-edge medicine, but doctors have been using genetics to assess risk of developing breast cancer for years. There are genetic tests that look for mutations of the BRCA 1 and BRCA 2 genes. Variations in these genes are linked to the rare and essentially purely genetic forms of breast cancer.

While detecting the BRCA variants is considered very valuable information to women with a family history of the disease, doctors and researchers knew genetics would one day play a bigger role in the remaining 95 percent of breast cancers. The deCODE BreastCancerTM test is aimed squarely at filling this gap, and to broadening the use of genetics in fight against breast cancer.

When a woman’s genome is scanned with deCODE BreastCancer, deCODE’s CLIA-registered laboratory checks for certain versions of seven single-letter variations in the genome, called SNPs. According to which versions are detected, that woman’s risk is then tallied, adding together the risk of each of the seven SNPs, to yield a score in relation to average risk, which is about 12% for American women of European origin. By multiplying the relative risk by the average, the results also provide a score of a woman’s absolute risk of developing breast cancer in her lifetime.

Depending upon a woman’s assessed risk, her doctor may suggest that she receive regular mammograms earlier than age 40, the standard starting age in the United States. If the test reveals a high risk, clinicians like Dr. Winsett might order a more advanced breast MRI or an ultrasound test for his patient. In some cases, high-risk patients with other contributing risk factors might start on a course of treatment to reduce the risk of tumors.

Decode’s breast cancer test is not a silver bullet. It won’t cure cancer. It measures risk and will be used in conjunction with other diagnostic tools and treatments to reduce the impact of the disease. But by using deCODE’s genetic test to find out which patients have a higher risk for the disease, says Dr. Winsett, earlier detection of breast cancer is possible.

“With the advent of deCODE’s breast cancer test we can intervene before the cancer happens. My hope is that we’ll see fewer breast cancers. I’m in business of dealing with breast lumps. I’m hoping this test can help reduce the breast lumps that I see.”

Mary Meets Dolly votes Constitution Party [Mary Meets Dolly]

Posted: 27 Oct 2008 12:32 PM CDT

I have been railing against Senator Barack Obama for several days now, but I have not mentioned who I am voting for.  All of my state's electoral votes will go to Obama, that is a certainty.  Considering what I write about here at Mary Meets Dolly, I cannot in good conscience vote for Senator McCain after he voted to use taxpayer dollars to fund embryo-destructive researchAs much as I like Sarah Palin, I am tired of the "lesser of the two evils."

So for the first time, I have been searching for a third party candidate that was truly 100% pro-life and not apologetic about it. I am very impressed with Chuck Baldwin of the Constitution Party and I believe that I will vote for him. I have meet him personally and I found him to be a man of principle and frankly a breath of fresh air.

Why am I even blogging about this when I know I am asking for all kinds of heat from my fellow pro-lifers who are pulling for McCain and Palin?  Because I want to introduce my readers to Dr. Baldwin and the Constitution Party.  Many pro-lifers know nothing about the party platform and I think they would be shocked to find that there is a truly pro-life party out there.  From the Baldwin08 website:

The pre-born child, whose life begins at fertilization, is a human being created in God's image. The first duty of the law is to prevent the shedding of innocent blood. It is, therefore, the duty of all civil governments, and that certainly includes the office of the President of the United States, to secure and to safeguard the lives of the pre-born. I affirm the God-given legal person hood of all unborn human beings, without exception.

In addition to guaranteeing the legal person hood of the unborn, Ron Paul's Sanctity of Life Act, which I wholeheartedly support, would strip the appellate jurisdiction of the Supreme Court in all cases of abortion in accordance with the U.S. Constitution, Article III, Section 2. This would mean that Roe v. Wade would immediately pass away as any legal authority on this issue. There would be no need to worry about putting a Supreme Court on the bench that might eventually make the right decision on this issue. We can, therefore, end legal abortion immediately upon enactment of the Sanctity of Life Act.

Republicans tout themselves as being "pro-life." Yet, the GOP controlled both houses of Congress and the White House for six years and did absolutely nothing to overturn Roe or end abortion-on-demand. If the Republicans were really serious about being pro-life the could have already ended legal abortion in America. Obviously the Republican Party and most GOP politicians are not serious about ending abortion, but are, regrettably, simply content to perpetuate the issue to manipulate pro-life voters.

Under my administration, we could end legal abortion in a matter of days, not decades. And if Congress refuses to pass Dr. Paul's bill, I will use the constitutional power of the Presidency to deny funds to protect abortion clinics. Either way, legalized abortion ends when I take office.

Here is a video of Chuck Baldwin for you to consider:

Server Issues [Eye on DNA]

Posted: 27 Oct 2008 11:46 AM CDT

Eye on DNA will be undergoing some server transitions within the next 48 hours so don’t be alarmed if the site is offline for a little while. Thank you!

It's been called a fruit fly for a long time, even if it's not technically right [adaptivecomplexity's blog]

Posted: 27 Oct 2008 11:06 AM CDT

In the aftermath of the Palin fruit fly comment, some bloggers are knocking people for not knowing that the model organism D. melanogaster is technically not a fruit fly.

But the fact is that the confusing nomenclature isn't some recent mix-up - as we see in the paper everyone's citing, biology textbooks as early as 1923 have referred to Drosophila as fruit flies, and

Among 13 textbooks published after 1945, with one exception all use fruit fly as the common name... Noteworthy is the finding that even the Entomological Society of America has been seduced. Its list of common names of insects assigns small (sic!) fruit flies to the Drosophlidae and other fruit flies to the Tephritidae.

So it's not unreasonable at all, when someone refers to "fruit fly research," to assume that this person is referring to one of the world's most widely used model organisms.

read more

Cardinal Egan says use your eyes [Mary Meets Dolly]

Posted: 27 Oct 2008 10:33 AM CDT

From Cardinal Egan's Just Look:

"The picture on this page is an untouched photograph of a being that has been within its mother for 20 weeks. Please do me the favor of looking at it carefully.

Have you any doubt that it is a human being?

If you do not have any such doubt, have you any doubt that it is an innocent human being?

If you have no doubt about this either, have you any doubt that the authorities in a civilized society are duty-bound to protect this innocent human being if anyone were to wish to kill it?

If your answer to this last query is negative, that is, if you have no doubt that the authorities in a civilized society would be duty-bound to protect this innocent human being if someone were to wish to kill it, I would suggest—even insist—that there is not a lot more to be said about the issue of abortion in our society. It is wrong, and it cannot—must not—be tolerated....

One day, please God, when the stranglehold on public opinion in the United States has been released by the extremists for whom abortion is the center of their political and moral life, our nation will, in my judgment, look back on what we have been doing to innocent human beings within their mothers as a crime no less heinous than what was approved by the Supreme Court in the "Dred Scott Case" in the 19th century, and no less heinous than what was perpetrated by Hitler and Stalin in the 20th. There is nothing at all complicated about the utter wrongness of abortion, and making it all seem complicated mitigates that wrongness not at all. On the contrary, it intensifies it.

Do me a favor. Look at the photograph again. Look and decide with honesty and decency what the Lord expects of you and me as the horror of "legalized" abortion continues to erode the honor of our nation. Look, and do not absolve yourself if you refuse to act."

Palin announces opposition to research on Homo sapiens [The Tree of Life]

Posted: 27 Oct 2008 09:30 AM CDT

Sarah Palin today has followed up her attack on fruit fly research by condemning much of the NIH Budget and a variety of other scientific earmarks.  At a town hall meeting yesterday while campaigning in Guam, Palin said
"We asked federal agencies to give us a summary of key words relating to research projects and we found an enormous number of them focused on homosapiens. I kid you not."
When asked by a teenage audience member to explain what was wrong with this research Palin said
"You probably are a homosapiens no? Or have many friends that are?  What we need to do is spend money on helping people change and not on studying these homosapiens"
The teen tried to respond but was escorted forcefully out of the hall by security while Palin continued on in her meeting.  At the end of the meeting Palin returned to the topic of science research and said "If elected, the McCain-Palin ticket will reallocate federal funds to eliminate waste on topics like homosapiens and fruit flies.  Enough is enough."

They are NOT fruit flies [evolgen]

Posted: 27 Oct 2008 09:00 AM CDT


In the recent kerfuffle over Sarah Palin's disparaging remarks about "fruit fly" research, an important point was missed by the general public, scientists, and even Drosophila geneticists: she wasn't talking about Drosophila. Now, this point has been clarified by a few people (notably Mike the Mad Biologist), and I think people are starting to get it. But it was remarkable how people automatically assumed she was talking about Drosophila.

Okay, maybe it wasn't so remarkable, given that even Drosophila researchers refer to these little insects as "fruit flies". The problem with that nomenclature is that Drosophila are not fruit flies. The olive fruit flies to which Palin was referring are true fruit flies (Tephritids), and these guys are major agricultural pests. She was actually criticizing applied research (as opposed to basic), which makes her comments even more absurd.

But everyone out there assumes that she's ragging on Drosophila research (which, for the most part, tends to be quite basic in nature -- note that basic does not imply worthless), even Drosophila geneticists. I've been notified of "Sarah Palin's attack on Drosophila" by multiple Drosophilists, only to point out to them that she wasn't going after us. Funny thing is, there is at least one Drosophila geneticist who also works on Bactrocera (the genus to which Palin's olive fly belongs): Michael Eisen. He's also fed about by the Drosophila/fruit-fly mix-up. And you should be too. The least we can hope for is that people who actually study Drosophila will know that they're not fruit flies.

Read the comments on this post...

Reader's Points and Clarification. [The Gene Sherpa: Personalized Medicine and You]

Posted: 27 Oct 2008 08:53 AM CDT

Dear Sherpa, I am an avid reader of your blog and quite often marveled by your great writing style. Today, however, I cannot resist to add another point to your list: The sherpa says and might be...

[[ This is a content summary only. Visit my website for full links, other content, and more! ]]

just another protein-interaction model [Reportergene]

Posted: 27 Oct 2008 08:44 AM CDT

ResearchBlogging.orgAndrea Pichler and colleagues from Mallinkrodt Institute of Radiology describe the generation of a transgenic Gal4-luc reporter mouse (G4F) that expresses the Firefly luciferase (from pGL3, Promega) under the regulatory control of a concatenated (5x) Gal4 promoter. The Gal4-luc strain, would allow noninvasive bioluminescence imaging of protein-protein interaction in vivo, a feature of real interest since traditional biochemical techniques often miss the detection of weak and transient interactions and, more often, return false positives. So, how does it work?
Protein interaction studies with Gal4-luc reporter mouse

Actually I'm quite frightened about this model: let I want to know whether protein X (bait) and Y (from library) interact in vivo. In order to detect XY interaction with the G4F mouse, I need to tag X with Gal4BD (get a X-Gal4BD expression vector) and then tag Y with VP16 (get a Y-VP16 expression vector). Then I have to make two more transgenics (and deal about positional effects) and, once I get them, backcrossing them in the G4F background and, like a juggler, breed and genotype three markers together. Three years are enough? Of course, an alternative would be to make transfections in vivo (i.e. with hydrodynamic somatic gene transfer or viral delivery) but even this job will need some validation (i.e. not seeing an interaction means that the interaction did not appear or it's a false negative due to problems in vector delivery. In conclusion protein-protein interaction is so hot and so hard matter, and my feelings are similar to those expressed for the Tango Assay:

There is a trend to interpret complex systems with complex conceptual design in today's molecular pharmacology. For sure this is geeky, funny, and sexy for mind, so it is worth being mentioned in Reportergene. Nevertheless I don't know whether this would be useful also to understand our inner biology. Managing three transgenes (also transiently) is not a joke. Using strong promoter to express receptors and cognate ones is unphysiological and very, very naive.

A. Pichler, J. L. Prior, G. D. Luker, D. Piwnica-Worms (2008). Generation of a highly inducible Gal4-Fluc universal reporter mouse for in vivo bioluminescence imaging Proceedings of the National Academy of Sciences, 105 (41), 15932-15937 DOI: 10.1073/pnas.0801075105

Ayurvedic Heavy Metal [Sciencebase Science Blog]

Posted: 27 Oct 2008 07:00 AM CDT

nagarjunaAyurvedic medicines can contain dangerous quantities of heavy metals, including lead, mercury, thallium and arsenic, clinical toxicologists in London have warned. Writing in the International Journal of Environment and Health, they suggest that recent European legislation aimed at improving safety of shop-bought products will have little impact on medicines prescribed by traditional practitioners, imported personally from overseas or bought over the Internet.

The problem is that the heavy metals are not simply inadvertent contaminants of natural herbal products, they are added deliberately in order to supposedly return the body to health by rebalancing allegedly essential minerals. You can read the full article on this via AlphaGalileo.

There are wide and wild claims for Ayurvedic medicine including the ability to treat diabetes, flue, cancer, asthma, flu, acne, boils, diarrhoea, headaches, and that perennial of the alternative remedy market, sex drive. Unfortunately, Ayurveda, although ancient, is no panacea.

Some practitioners are hoping to modernise the Ayurvedic system. However, until it is more widely recognised among users that adding arsenic, lead, thallium and other potentially toxic heavy metals to so-called medicinal preparations is unacceptable, it will remain a practice more associated with the past than contemporary medicine.

Paul I. Dargan, Indika B. Gawarammana, John R.H. Archer, Ivan M. House, Debbie Shaw, David M. Wood (2008). Heavy metal poisoning from Ayurvedic traditional medicines: an emerging problem? International Journal of Environment and Health, 2 (3/4), 463-474

Ayurvedic Heavy Metal

Revising the NIH Grant Review Process [Bitesize Bio]

Posted: 27 Oct 2008 05:02 AM CDT

With a provocative suggestion, Mike the Mad Biologist proposed the idea of Top-down NIH leadership to determine where research funding should be allocated.

The point is that, as DrugMonkey noted, it’s too difficult for reviewers or program officers to reject proposals based on their unsuitability for the goals of NIH, since these goals, even within certain areas, are too broadly defined. My experience has been that with very targeted calls for proposals, there are far fewer proposals submitted, and it’s much easier to flat out reject them because many proposals are not germane to the funding objectives. This means that NIH program officers have to be far more active in defining specific research objectives than they have been–to a considerable extent, NIH is placing this responsibility on reviewers who often lack knowledge of the larger institutional objectives. That needs to be changed.

Drug Monkey also addresses the problem of NIH grant reviewers who focus too much on grantsmanship.

The reason is that this policy does nothing about the tendency of reviewers to focus on grantsmanship issues as an easy triage mechanism, instead of taking the “fish or cut bait” hard look at the genuinely new application the first time. The primary stage of review is the main driver here. The ameliorative measures should have accounted for the source of the problem and tried to address it more directly. The single amendment limit doesn’t do this.

One of the ways the original goal ["to ensure earlier funding of high-quality applications and improve efficiencies in the peer review system"] could be accomplished would be through reviewer education and instruction. Put the data figures in front of all reviewers and say “Bad dog! Stop deifying revision status and grantsmanship. Focus on the underlying science. What will really be accomplished through the review process- changes in the proposal only? or actual changes in the resulting science?”

I don’t think too many people will agree with Mike on this one - as one commenter notes, “I could easily list multiple top-down NIH programs under way right now - spending hundreds of millions of NIH money - that are mostly or completely wasteful.”

And while Drug Monkey’s suggestion of “reviewer education and instruction” is much needed, I would guess that it also won’t completely address the problem that reviewers may be overwhelmed by the sheer number of grant applications.

Not that I have a better suggestion. It’s a tough problem, which Drug Monkey puts his finger on in quoting the NIH press release on changes in revision policy:

NIH analysis indicates that an increasing number of meritorious applicants that were ultimately funded had to resubmit their applications multiple times which increased burden on applicants and reviewers alike. … data reveals a reduction in the number of awards made to original applications. An increasing number of projects were funded only after one or more resubmissions. This trend has been increasing over recent years.

Free subscription to Nature? [Reportergene]

Posted: 27 Oct 2008 03:34 AM CDT

Reportergene has joined forces with to offer to the reportergenomist community a new, exciting, and entirely free resource. Visit today to browse a selection of complimentary Biotechnology and Pharmaceutical magazines, white papers, webinars, podcasts, and more. No credit cards, coupons, or promo codes required.

Do you qualify?* Try it today!

*Only publisher is responsible to accept your application, anyway this is not a privacy-trap: some months ago I have applied to some offers and finally I successfully received a complimentary subscription to Biotechniques, to Biophotonics, and even to Nature Methods. It works!

Top 10 Genomics News from - Week of 19 Oct 08 [Think Gene]

Posted: 27 Oct 2008 01:00 AM CDT

"Science Spore?" [Genomicron]

Posted: 25 Oct 2008 09:09 PM CDT

I came across this interesting forum on Spore. I hope SpongB6F1 won't mind if I quote this posting at length, as I think it is very insightful.
"Science Spore" would be ideal.


I think many people will claim that although some kind of abstract commitment to science would have been nice in Spore, what they really want is just some decent, engaging and clever gameplay, instead of a rigid pattern of repetitive, simplistic grinding tasks.

But I think these are two very interrelated issues. The gameplay elements that attracted many of us to the game were precisely the "sciencey" parts. Because by science we're not talking about the propounding of abstract theorems or doing calculus problems here--the science parts most of us want are basically just the interesting game mechanics everyone is talking about (e.g. functional consequence to parts placement in Creature, or a more realistic Creature ecosystem and behavior system, or any number of sci-fi features we wanted in Space, etc.).

These are science-related not because of any didactic teaching of facts, but in their basic nature and the mental approach you'd have to take to them. Such as trial and error, experimentation, exploration of the world, problem solving, inducing general principles of how the world works, etc. E.g. figuring out what kinds of creature design would be effective. Figuring out what kinds of creature behaviors and strategies are appropriate for which niche, etc.

So in asking for a "Science Spore," most of us are really asking for a game that actually engages our minds on some level. That's why we play games in the first place.

I am, of course, pleased to see that many others are interested in a game like Spore that incorporates some actual evolution, and that there is even hope that this will arrive in the form of an expansion or sequel someday. But would there be a market?

My favourite games. [Genomicron]

Posted: 25 Oct 2008 06:56 PM CDT

One of the reasons I was interested in giving some comments on the science in Spore is that I am a big fan of video games but rarely have a chance to play anymore. The discussion about Spore (which I wasn't asked to evaluate as a game per se) got me thinking back on the games I have really enjoyed playing. So, just for fun, I have come up with this list of some of my favourite games. Now, these go back to my elementary school days in the 1980s, so bear with me. It's a mix of console and computer games and is a little behind the times as I don't have much time for games anymore. Here they are largely in chronological order.

1. Gorf, Advanced Dungeons & Dragons, Baseball, and Tron: Deadly Discs

Included for nostalgic reasons, these are some of my favourite games from the first consoles we owned when I was very young. Gorf on the Commodore VIC-20, and then Advanced Dungeons & Dragons and Baseball (Yer out!) on Intellivision. My father and I played baseball until our hands hurt (not hard on the awkward controllers). I once (and only once) got 1,000,000 points on Tron: Deadly Discs and got to see the Guardians. (Just outside this list: Astrosmash).

2. Super Mario Bros. (I and III), Metroid, and Legend of Zelda

My cousins are part Japanese and had Nintendo at home two years before it came out in North America -- when it finally arrived, I had to get one specifically to play Super Mario Bros. Later, I went to see the crappy movie The Wizard just for the advance footage of Super Mario 3 (worth it) and I spent $80 of my tips from working as a busboy to get it as soon as it was released (worth it). And no, I don't need warp zones to finish either of them. Absent from this list: Super Mario 2. Metroid and Zelda also consumed many hours of my youth.


I pretty much got a Game Boy just for this game, having become hooked on it in the arcade. Easily one of the greatest games made.

4. Wing Commander (I, III, and Prophecy)

I don't usually like flight sims, but space ones I do. We played this game a lot in high school. So much, in fact, that we once left Wing Commander running on a computer in one of the classrooms, but managed to convince the teacher that it was a screen saver. It only got better with WCIII. Mark Hamill as Blair? Awesome.

5. Mortal Kombat

My buddy and I could finish this on one quarter when we were undergrads (yep, games used to cost 25c). Of course, we spent a lot more getting to that point. FINISH HIM! (Over, down, over, high punch).

6. Doom (I and II)

Not so scary now, but back then playing with the lights out and the sound up was a challenge.

7. StarCraft

This game is still popular and there is even a professional league dedicated to it.

8. Perfect Dark

This game was great for playing with my brother on his Nintendo 64. For starters, you could be on the same team and fight simulated agents. Is anything cooler than a laptop gun?

9. Warcraft III

This realtime strategy had amazing cut scenes and extraordinary gameplay along with an exceptional story line.

10. Halo

One of the best selling games ever, and for good reason.

Ok, your lists?

The Science of Spore [Genomicron]

Posted: 25 Oct 2008 01:11 PM CDT

Is Spore meant to be just a game, with no suggestion that it has scientific content?

Fruit flies. I kid you not. [Genomicron]

Posted: 25 Oct 2008 11:24 AM CDT

I have complained recently about the state of basic research support in Canada, as the current government is pushing for more short-sighted, applied, industry-oriented work. This is as nothing compared to the attitude of some politicians south of the 49th.

Here is how a recent paper of mine began*:
Through all the major transitions in genetics over the past 100 years – from early mutation and mapping studies involving countless crosses and phenotypic analyses, to karyotyping and polytene chromosome banding, to the application of allozymes in population-level surveys, to the advent of complete genome sequencing and the rise of "evo-devo" – the fly Drosophila melanogaster has maintained its uncontested status as a preeminent model organism (Brookes, 2001; Beller & Oliver, 2006). Several entire volumes have been devoted to its use in experimental genetics (e.g., Demerec & Kaufmann, 1996; Powell, 1997; Sulivan et al.,2000; Henderson 2003; Ashburner et al., 2005), and it is estimated that there are well over 1,000 research groups worldwide who use Drosophila as a key model (Clark et al., 2003). As Demerec & Kaufmann (1996, p.1) put it, "it would not be an exaggeration to say that we have learned more about the basic laws of heredity from the study of this fly than from work on all other organisms combined."
Here is what Palin has to say about wasting money on fruit fly work. I kid you not.


* Yes, I know Drosophila technically is not a fruit fly, but it is often referred to this way.


It is even worse... apparently this actually referred to applied studies on the olive fruit fly (Bactrocera oleae) which is a major agricultural pest (one can only imagine what she says about basic research).

Here is what the Congressman who earmarked it stated:
"The Olive Fruit Fly has infested thousands of California olive groves and is the single largest threat to the U.S. olive and olive oil industries," he said. "I secured $748,000 for olive fruit fly research and irradiation in the (fiscal year 2008) appropriations bill for the U.S. Department of Agriculture. The USDA will use some of that funding for their research facility in France. This USDA research facility is located in France because Mediterranean countries like France have dealt with the Olive Fruit Fly for decades, while California has only been exposed since the late 1990s. This is not uncommon; the USDA has several international research facilities throughout the world, including Australia, China and Argentina."

Hat tips: Pharyngula, Chance and Necessity, Mike the Mad Biologist

Evolution: Education and Outreach special issue -- evolution of eyes. [Genomicron]

Posted: 25 Oct 2008 07:30 AM CDT

I was planning to wait until the issue was actually in print, or at least until all the articles were available in preprint, but there is already some buzz starting so here it is. The upcoming issue of Evolution: Education and Outreach, of which I was editor, is a special issue dedicated to eye evolution. The table of contents:

Evolution: Education and Outreach
Volume 1 Issue 4
The evolution of eyes
Edited by T. Ryan Gregory


1. Introduction by T. Ryan Gregory

2. Casting an Eye on Complexity by Niles Eldredge

Original science / evolution reviews

3. The Evolution of Complex Organs by T. Ryan Gregory

4. Opening the "Black Box": The Genetic and Biochemical Basis of Eye Evolution by Todd H. Oakley and M. Sabrina Pankey

5. A Genetic Perspective on Eye Evolution: Gene Sharing, Convergence and Parallelism by Joram Piatigorsky

6. The Origin of the Vertebrate Eye by Trevor D. Lamb, Edward N. Pugh, Jr., and Shaun P. Collin

7. Early Evolution of the Vertebrate Eye—Fossil Evidence by Gavin C. Young

8. Charting Evolution's Trajectory: Using Molluscan Eye Diversity to Understand Parallel and Convergent Evolution by Jeanne M. Serb and Douglas J. Eernisse

9. Evolution of Insect Eyes: Tales of Ancient Heritage, Deconstruction, Reconstruction, Remodeling, and Recycling by Elke Buschbeck and Markus Friedrich

10. Exceptional Variation on a Common Theme: The Evolution of Crustacean Compound Eyes by Thomas W. Cronin and Megan L. Porter

11. The Causes and Consequences of Color Vision by Ellen J. Gerl and Molly R. Morris

12. The Evolution of Extraordinary Eyes: The Cases of Flatfishes and Stalk-eyed Flies by Carl Zimmer

13. Suboptimal optics: vision problems as scars of evolutionary history by Steven Novella (coming soon)

Curriculum articles

14. Losing Sight of Regressive Evolution by Monika Espinasa and Luis Espinasa

15. Misconceptions About the Evolution of Complexity by Andrew J. Petto and Louise S. Mead

16. Bringing Homologies Into Focus by Anastasia Thanukos

Book reviews

17. Jay Hosler, An Evolutionary Novelty: Optical Allusions by Todd H. Oakley

PZ Myers is coming to town. [Genomicron]

Posted: 25 Oct 2008 07:19 AM CDT

In support of my hypothesis that PZ Myers had several clones of himself produced so that he could travel all around while still teaching courses, I noted a poster on my way to the lab yesterday that indicates that he will be in Guelph on Saturday Nov. 1, speaking in Thornbrough 1200 at 2 pm. Cost will be $2 (that's a bargain -- only $1.60 US!). This time I will actually try to attend, having skipped the Evolution 2008 conference in his part of the world.

1 comment:

Teff john said...

In the early years of the International Human Genome Project, DNA sequencing was done using gel electrophoresis, a technique that was heavily labour-intensive and rather prone to errors.Then in 1998, a new technique called capillary sequencing became available through a machine called the Applied Biosystems Inc. 3700, which allowed greater quantities of DNA to be sequenced at lower cost, with far less human involvement, and with a lower error rate. This ushered in "high throughput" sequencing and allowed the human genome to be sequenced far faster than had originally been thought possible when the Human Genome Project was started.
teff john