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Thursday, October 16, 2008

Nobel Laureates: Christiane Nüsslein-Volhard and Eric Wieschaus

 

The Nobel Prize in Physiology or Medicine 1995.
"for their discoveries concerning the genetic control of early embryonic development"


Christiane Nüsslein-Volhard (1942 - ) and Eric F. Wieschaus (1947 - ) received the Nobel Prize in Physiology or Medicine for their contribution to understanding the genetics of development in the fruit fly, Drosophila melanogaster.

Their main contribution was to identify a number of genes that controlled the development of the embryo. The approach was to create mutations at random then screen large numbers of flies for recessive lethals affecting various stages of early embryogenesis. The initial large scale experiment was carried out at the EMBL Labs in Heidleberg, Germany. They established 27,000 lines containing mutated chromosomes and characterized 139 mutations affecting embryogenesis. Of these, 15 were described in the classic 1980 Nature paper. (See Silver Screen, a tribute to the paper on it's 25th anniversary.)

The original 15 genes were: cubitus interruptus, wingless, gooseberry, hedgehog, fused, patch, paired, even-skipped, odd-skipped, barrel, runt, engrailed, Kruppel, knirps, and hunchback. To anyone familiar with the field this reads like a who's who of Drosophila development. Dozens (hundreds?) of papers have been published on each of these genes.

The experimental approach is described in the Press Release below. I am only including the part that refers to Nüsslein-Volhard and Wieschaus. They shared the prize with Edward Lewis.

THEME:
Nobel Laureates
Brave decision by two young scientists

Christiane Nüsslein-Volhard and Eric Wieschaus both finished their basic scientific training at the end of the seventies. They were offered their first independent research positions at the European Molecular Biology Laboratory (EMBL) in Heidelberg. They knew each other before they arrived in Heidelberg because of their common interest: they both wanted to find out how the newly fertilized Drosophila egg developed into a segmented embryo. The reason they chose the fruit fly is that embryonic development is very fast. Within 9 days from fertilization the egg develops into an embryo, then a larvae and then into a complete fly.

Fig. 1 Regions of activity in the embryo for the genes belonging to the gap, pair-rule, and segment-polarity groups. The gap genes start to act in the very early embryo (A) to specify an initial segmentation (B). The pair-rule genes specify the 14 final segments (C) of the embryo under the influence of the gap genes. These segments later acquire a head-to-tail polarity due to the segment polarity genes.

They decided to join forces to identify the genes which control the early phase of this process. It was a brave decision by two young scientists at the beginning of their scientific careers. Nobody before had done anything similar and the chances of success were very uncertain. For one, the number of genes involved might be very great. But they got started. Their experimental strategy was unique and well planned. They treated flies with mutagenic substances so as to damage (mutate) approximately half of the Drosophila genes at random (saturation mutagenesis). They then studied genes which, if mutated would cause disturbances in the formation of a body axis or in the segmentation pattern. Using a microscope where two persons could simultaneously examine the same embryo they analyzed and classified a large number of malformations caused by mutations in genes controlling early embryonic development. For more than a year the two scientists sat opposite each other examining Drosophila embryos resulting from genetic crosses of mutant Drosophila strains. They were able to identify 15 different genes which, if mutated, would cause defects in segmentation. The genes could be classified with respect to the order in which they were important during development and how mutations affected segmentation. Gap genes (Fig 1) control the body plan along the head-tail axis. Loss of gap gene function results in a reduced number of body segments. Pair rule genes affect every second body segment: loss of a gene known as "even-skipped" results in an embryo consisting only of odd numbered segments. A third class of genes called segment polarity genes affect the head-to-tail polarity of individual segments.

The results of Nüsslein-Volhard and Wieschaus were first published in the English scientific journal Nature during the fall of 1980. They received a lot of attention among developmental biologists and for several reasons. The strategy used by the two young scientists was novel. It established that genes controlling development could be systematically identified. The number of genes involved was limited and they could be classified into specific functional groups. This encouraged a number of other scientists to look for developmental genes in other species. In a fairly short time it was possible to show that similar or identical genes existed also in higher organisms and in man. It has also been demonstrated that they perform similar functions during development.


[Photo Credits: Nüsslein-Volhard - Encylopaedia Britanica, © Patrick Piel/Gamma Liaison, Wieschaus -News at Princeton]

Fair Vote Canada Election Results

 
Here's what the result would have been with a nation-wide proportional system from Fair Vote Canada.

Conservatives - 38% of the popular vote: 117 seats (not 143)
Liberals - 26% of the popular vote: 81 seats (not 76)
NDP - 18% of the popular vote: 57 seats (not 37)
Bloc - 10% of the popular vote: 28 seats (not 50)
Greens - 7% of the popular vote: 23 seats (not 0)
I don't favor such a system. I like the Mixed Member Proportional MMP) system based on provinces.

The British Columbia referendum on the Single Transferable Vote (STV) system for provincial elections is set for May 12, 2009. 58% of voters supported the new voting system in the last referendum (2005). This was just short of the required 60%. It is very likely that the new proportional system will be adopted this time around, making British Columbia the first of many provinces to enter the 21st century.


Wednesday, October 15, 2008

Nigeria Has Competition

 
I just got this email message and I thought I'd share it with the rest of you. All my money is tied up in deals with Nigerians and investments in Viagra so I can't take advantage of this fabulous offer.

I expect to be flush with cash by next week because I just won the European lottery but I'll be spending most of it to enlarge one of my vital organs.
Hello Pal,

I hope my email fine you well. I am in need of your assistance. My name is Sgt. Jarvis Reeves. I am an American soldier serving in the 1st Armored Division in Iraq, we have just been posted out of Iraq and to return in a short while. My colleague and I need your help to transfer out the sum of Twenty Five Mllion U.S Dollars ($25 MUSD). If you are interested I will furnish you with more details

As awair your response.
Email:sgt.jr@hotmail.com

Yours,
Sgt. Jarvis Reeves

God Bless America!!


Tuesday, October 14, 2008

Move to Canada

 



[Hat Tip: The Unexamined Life]

Bacteria Phylogeny: Facing Up to the Problems

There are millions of species of bacteria. Sorting out their evolutionary history has been a major challenge for decades. Unlike the much bigger, multicellular, eukaryotes, there are few morphological markers to assist scientists in classifying bacteria. The fossil record is mostly silent.

Molecular evolution came to the rescue thirty years ago when cloning and sequencing became common. Soon there were elaborate and detailed phylogenetic trees based on comparing sequences of conserved genes from many species.

The gene of choice was the one for the small subunit ribosomal RNA (SSU rRNA). This gene was well conserved in bacteria and it was easy to get sequences simply by PCR. (The ends of the SSU rRNA gene are conserved and this means that you can develop universe primers for PCR.)

Over the years, the SSU rRNA gene has become what is called the "gold standard" in bacterial phylogeny and taxonomy. Many species have been assigned to taxa based entirely on the sequence of their SSU rRNA gene. Unfortunately, the "gold standard" has become somewhat tarnished lately.

Our fellow blogger, Jonathan Eisen of The Tree of Life, has recently published a paper that looks at the problems with bacterial phylogeny (Wu and Eisen, 2008). He posted a brief summary of the paper and commented on why he likes the journal Genome Biology [Happy Open Access Day: Back to Genome Biology for Me].

ResearchBlogging.orgThere is much to like about this paper. The authors face up to the problems with the current bacterial phylogeny, which is based almost entirely on a single gene (SSU rRNA). They point out that this is risky given what we know about molecular phylogenies. Furthermore, in the case of the SSU ribosomal RNA gene we know for a fact that this has led to problems and inconsistencies. In addition to the practical difficulties there are good theoretical reasons for being suspicious of phylogenies constructed from nucleotide sequences.

What to do? One possible solution is to abandon SSU rRNA as a "gold standard" and replace it with a highly conserved protein coding gene. Unfortunately, this doesn't get around the problem of relying on a single gene. The way around this is to use an artificial concatenated sequence made up of several different conserved genes laid out end-to-end in one large string of amino acids.

So why isn't this done? Because, as Wu and Eisen point out, it ain't that easy. The main difficulty in any phylogenetic study is getting a proper alignment. This is a problem that many workers simply ignore when they use automated alignment software like CLUSTALW. These workers assume that the alignments are valid.

They aren't, and this is another example of facing up to the problem. Many scientists agonize over what program to use when constructing their trees—should they use maximum likelihood, parsimony, etc. etc.? In most cases these decisions are a complete waste of time because their alignments aren't good enough to make a difference.

Here's how Wu and Eisen explain it ...
It has been shown that alignment quality can have greater impact on the final tree than does the tree-building method employed [20]. Therefore, preparing high quality sequence alignments is a most critical part of any molecular phylogenetic analysis. This preparation typically involves careful but tedious manual editing and trimming of the generated alignments, and thus remains the biggest challenge to automation. When scaling up this process, the trimming step is often simply ignored. Automated trimming based on the number of gaps in each column or each column's conservation score can be used to select conserved blocks, but still is not satisfactory when a high quality tree is required.
Keep in mind that what is being proposed is a large tree based on concatenated sequences from many genes. You don't want to do multiple sequence alignments for every gene by hand, and yet up until now, that was the only way to get accurate results.

Wu and Eisen have written a program called AMPHORA that hopefully solves this problem. They begin by manually creating "seed alignments" that are manually curated. Then they use AMPHORA to align all the other sequences to the seed alignments. In this way they hope to overcome the limitations of automated multisequence alignment without having to align everything by hand.

None of this would be possible, of course, unless there were large numbers of species where every one of the target genes have been cloned and sequenced. In the 20th century this would have been impossible but now there are hundreds of completely sequenced bacterial genomes. This means that each one of them has a sequenced copy of the genes required for this kind of analysis.

All that's left is to identify the completely sequenced genomes and pick the set of genes. There are 578 genomes in the database but many of these are close relatives that will not be useful in constructing a large tree of all bacterial sequences. The final set contains 310 genomes with representatives of all the major groups.

The authors selected 31 genes for their initial proof of principle paper (dnaG, frr, infC, nusA, pgk, pyrG, rplA, rplB, rplC, rplD, rplE, rplF, rplK, rplL, rplM, rplN, rplP, rplS, rplT, rpmA, rpoB, rpsB, rpsC, rpsE, rpsI, rpsJ, rpsK, rpsM, rpsS, smpB, tsf). Those of you who recognize these genes will see that 21 of them are small ribosomal proteins. This was not the best choice, in my opinion, but the authors of the paper note that they are continuing the study by incorporating better genes such as HSP70 (dnaL) and EF-Tu (tufA). You can't just choose any conserved gene because it has to be present in most species and there are surprisingly few genes that meet that criterion.

After all that, what's the bottom line? The grand phylogeny is shown at the top of this posting. It resolves many groups that are unresolvable using the SSU rRNA tree. In some cases this tree reveals species that have been incorrectly assigned to higher taxa. These species will have to be reclassified if this result holds up.

The most important finding is that the method works and it yields trees with excellent resolution of the major bacterial taxa.


Wu, Martin, Eisen, Jonathan (2008). A simple, fast, and accurate method of phylogenomic inference Genome Biology, 9:R151 [Genome Biology] [doi:10.1186/gb-2008-9-10-r151]

Gene Genie #38

 
The 38th edition of Gene Genie has been posted at ScienceRoll [Gene Genie: Back in Action!].
Gene Genie is the blog carnival of clinical genetics and personalized medicine. Enjoy the numerous posts and articles focusing on these interesting fields of medicine. We dedicate this carnival edition to genetic testing, SNP watch and DNA.
The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

Here are all the previous editions .....
  1. Scienceroll
  2. Sciencesque
  3. Genetics and Health
  4. Sandwalk
  5. Neurophilosophy
  6. Scienceroll
  7. Gene Sherpa
  8. Eye on DNA
  9. DNA Direct Talk
  10. Genomicron
  11. Med Journal Watch
  12. My Biotech Life
  13. The Genetic Genealogist
  14. MicrobiologyBytes
  15. Cancer Genetics
  16. Neurophilosophy
  17. The Gene Sherpa
  18. Eye on DNA
  19. Scienceroll
  20. Bitesize Bio
  21. BabyLab
  22. Sandwalk
  23. Scienceroll
  24. biomarker-driven mental health 2.0
  25. The Gene Sherpa
  26. Sciencebase
  27. DNA Direct Talk
  28. Greg Laden’s Blog
  29. My Biotech Life
  30. Gene Expression
  31. Adaptive Complexity
  32. Highlight Health
  33. Neurophilosophy
  34. ScienceRoll
  35. Microbiology Bytes
  36. Human Genetic Disordrs
  37. The Genetic Genealogist
  38. ScienceRoll


Have Fun on Voting Day

 
Here's a video to keep you happy as you hold your nose and go to the polls (in Canada). There's a metaphor in it somewhere but I can't for the life of me figure it out. Maybe it has something to do with where my vote is going?




[Hat Tip: psa at Canadian Cynic. Jennifer Smith at Runesmith's Canadian Content had the same idea I had about linking the video to voting day.]

PZ Myers in Toronto

 
Email me if you would like to meet PZ before his talk on Friday afternoon.



Monday, October 13, 2008

Strategic Voting

 
Damn.

The Canadian election is tomorrow and I had almost made up my mind to vote for the Liberal candidate in my riding. He's a man I can respect and he will be a much better member of parliament than the Conservative candidate.

Up until last week I was considering a vote for the New Democratic Party because their policies are close to my personal position. Also, I wanted to send a message to Stéphane Dion, who I don't think is up to the job as leader of the Liberal party. I realized that my vote might result in the election of the Conservative candidate in my riding since the race between the Conservative challenger and Liberal incumbent is very close. That risk was worth it, in my opinion, because Stéphane Dion needed to lose in order to resign from the leadership.

The latest poll results indicate that the Conservatives might win a majority and I don't want that to happen. So I decided to vote Liberal, hoping that the events of the election campaign would be enough for Stéphane Dion. When he loses tomorrow he will resign.

At least that's what I thought until I read this morning's newspapers [The Canadian Press].
"I will never quit. I will stay for my country," the Liberal leader said Sunday during a last swing through southeastern Ontario before flying off on a frenetic coast-to-coast tour seeking the NDP and Green votes he desperately needs.

"But I'm working hard now. We're working all of us for a victory, for a progressive government. This is what is at stake."

When pressed on how he would respond if Liberal rivals push to oust him, a chippy Dion raised his voice.

"I'm the leader! I am the leader. And I'm working to win. I'm not a quitter."

...

Dion's strident tone may raise eyebrows in Liberal circles where private reaction to his campaign performance has typically ranged from tepid praise to hand wringing. Dion, a political scientist and former professor of public administration, has a reputation for tenacity and a mile-wide stubborn streak.

He is set to face a Liberal party leadership review next spring.
That's it for me. I'm voting NDP and I'm going to tell my Liberal candidate exactly why I'm doing it. If the only way to save the Liberal party is for Dion to quit ASAP and if the only way that will happen is if he's kicked out, then it looks like the Liberals are going to have to lose a lot of seats before they get the message.

I'll suffer the short term pain for the long term gain.


Monday's Molecule #92

 
Today's molecule is a cartoon drawing of an image that depicts something very important. Your task is to explain what the image shows. Then you have to explain why this is important when it comes to describing the function of something called a "balancer."

It's a short step from there to this weeks Nobel Laureates. They used balancers in their work.

You need to describe what you see in the cartoon as accurately as possible and name the species. Then identify the Nobel Laureates, taking care to name only those ones who might have used balancers in their prize winnning work.

The first one to correctly identify the molecule and name the Nobel Laureate(s), wins a free lunch at the Faculty Club. Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week's reward. You know who you are.

THEME:

Nobel Laureates
Send your guess to Sandwalk (sandwalk (at) bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and names the Nobel Laureate(s). Note that I'm not going to repeat Nobel Laureate(s) so you might want to check the list of previous Sandwalk postings by clicking on the link in the theme box.

Correct responses will be posted tomorrow. I reserve the right to select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: This weeks winner is Bill Chaney from Nebraska. He recognized that the "molecule" depicted a chromosomal inversion in a Drosophila chromosome. Such inversions are a characteristic of balancer chromosomes. Balancers are used in maintaining fly stocks, especially ones carrying homozygous lethal mutations.

The Nobel Laureates must be Christiane Nüsslein-Volhard and Eric Wieschaus


Are Science and Religion Compatible?

 
I've been somewhat remiss in posting for a few days as I've been catching up on some reading and discussing science and religion with my friends.

The question that interests me is whether basic religious tenets are compatible with science, where "science" is defined as a way of knowing—a way that combines evidence and rational thinking to come up with "truths" about the universe we inhabit.

It seems obvious to me that there are some forms of deism that do not conflict with science. Is that it?1 Are there any other versions of religion that maintain an appropriate distance from science?

I'd like to hear from people who are religious but not deists. Can they give me some example of their religious claims that do not in any way conflict with science? I'm thinking specifically of those religions that promote belief in a personal God.


1. Buddhism may count if it's the form of Buddhism that doesn't believe in supernatural beings. I don't call that a religion.

Activist Scientists

 
We seem to have forgotten that scientists can be social activists. In my time it was common for scientist to take an active role in social causes. It was the time of "Science for the People" and similar organizations. Very little remains of that kind of activism, David Suzuki is just about the only one of those scientists who is still trying to change the world. Some of them have become administrators and advisers to Presidents.

Given the antagonism that greets modern scientists who step out of line (i.e., Richard Dawkins) I can understand why social activism is out of favor.

I was reminded that in the early part of the last century, there were scientists who took up social causes. I happened to stumble on the website of my colleague, Donald Forsdyke of Queen's University [Haldane's Rule]. Here's one of the photographs from that site.

JBS Haldane addressing a 'United Front' meeting in January 1937. Photograph from the Sun newspaper reproduced in Ronald Clark's 1968 biography of Haldane, published by Hodder & Stoughton.
It's hard to picture any of today's most prominent scientist in such a scene. Perhaps the "United Front" movement1 is too liberal for the average scienist?


1. It was a socialist movement with strong ties to Marxism as a philosophy and communism as an economic and political strategy

Saturday, October 11, 2008

Why Do We Call them IDiots? (Part CCCLXVII)

 
Rebecca of Skepchick writes about a YouTube fight involving a creationist.
You know what’s hilarious? Seeing a jerk get schooled. You know what’s even funnier? When the jerk happens to be a creationist who has spent a lot of time and effort filling YouTube with the same old oft-debunked creationist garbage we see all the time, and who then illegally attempts to silence his rational critics.

I’ve been following the fight between creationist VenomFangX and pure awesomeness Thunderf00t for quite some time. For an overview, watch some of Thunderf00t’s excellent series, “Why Do People Laugh at Creationists?” VFX shows up a LOT. This upset him quite a bit.

Basically, VFX filed DMCA takedown notices on Thunderf00t’s videos, despite the fact that VFX knew those notices were false and malicious. This is illegal, and Thunderf00t obtained clear proof of the action. He could have sued the living pants off VFX and had him banned permanently from YouTube, but instead, he did this:



Epigenetics, Again

 
The National Institutes of Health (NIH) have launched a $190 million research effort to learn about epigenetics. According to Nature News ...
It’s not that epigenetics is totally useless. I just don’t see why it’s worth 190 million dollars.

Kevin Struhl
Harvard Medical School
Epigenetics, described as "inheritance, but not as we know it"1, is now a blisteringly hot field. It is concerned with changes in gene expression that are typically inherited, but not caused by changes in gene sequence. In theory, epigenetic studies can help explain how the millions of cells in the human body can carry identical DNA but form completely different cell types, and perhaps why certain cells are susceptible to disease.

The NIH's epigenomics initiative is a plan for such studies on a grand scale including, for example, surveys in different human cell types of all the chemical tags, or epigenetic marks, that might control genes.
It seems strange to be spending so much research money on something that scientists can't even define properly [Epigenetics in New Scientist, Epigenetics Revisited, Epigenetics]. Perhaps some of this money will go toward coming up with a reasonable definition of what they're studying.

As far as I know we already have a good model for how totipotent cells can differentiate into many different cell types. We also understand how they can revert to pleuripotent cells. We even know that differentiated cells can be transformed back into stem cells by adding certain transcription factors.

Now we add in the fact that some DNA binding proteins can covalently modify DNA and this affects gene expression. What's the big deal?


Friday, October 10, 2008

Humanism Is "Liberal"

 
I'm not a humanist and now I know why. Not only is it immoral and atheist but it's also (gasp!) LIBERAL! Now I know why the Christians are so frightened.




[Hat Tip: Friendly Atheists]

P.S. I don't make fun of spelling errors because people in glass houses ....

P.P.S. As strange as it may seem to our neighbors to the south, in Canada we not only have a Liberal Party but people actually vote for it!