apalazzo | November 30, 2006I forgot to bring this up yesterday. Science conducted a review of it's publishing practices (due to the whole cloning affair). Honestly it would have been hard for them to have prevented this. In the end the best check on a scientist's work is reproducibility. But the review board did recommend something I like very much. From a NY Times article in yesterday's paper:
... authors should specify their individual contributions to a paper, a reform aimed at Dr. Hwang's stratagem of allowing another researcher, Gerald Schatten of the University of Pittsburgh, to be lead author of one of the…
apalazzo | November 30, 2006There was some minor controversy for the RNAi Nobel ... should Rich Jorgensen's have been acknowledged? and the miRNA people?
Here is what Rich Jorgensen has to say (from the latest edition of Science):
I feel that the Nobel committee's decision to focus on the central role of double-stranded RNA (dsRNA) was quite appropriate; it was this specific discovery that broke an obscure field wide open and brought it to the attention of all biologists. The publication of RNAi (1) catalyzed new interactions between plant and animal geneticists that led directly to all kinds of discoveries about the…
apalazzo | November 29, 2006OK I finally did that experiment that people asked for ... and more.
If you want to know why I performed this experiment, read this post on RNA treatments for autism. Here I present to you evidence that your body is secreting enzymes, called RNAses, that will chew up your RNA in minutes.
So the experiment:
500ng of RNA was mixed with either
- control buffer (100mM KCl, 10mM Tris buffer pH7.4)
- 1ul of DNAse (1mg/ml), this is what you would call a negative control - no degradation should be seen here
- 1ul of water applied to sweaty skin
(After working a bit with my latex gloves, I puled off…
apalazzo | November 29, 2006
When I was a grad student, eukaryotes had all the neatest toys ... actin, microtubules, kinesins, dynein, myosin, dynamin, SNAREs ...
OK that's not totally true - bacteria had their version of tubulin (the constituent of microtubules), and it's called FtsZ. Then others found that bacteria had a version of actin, the most known is called MreB. The latest is that prokaryotes have dynamin. (Click here for previous dynamin entries.)
From the paper:
Given the presence of large GTPases with predicted dynamin-like domain organization in many members of the Eubacteria such as E. coli and Bacillus…
apalazzo | November 27, 2006
I mostly agree with Tyson ...
[Here's a different take on the whole culture-war phenomenon, what we scientists need to fight aggressively for is tolerance ... tolerance for ATHEISTS. On this front Dawkins is losing ground.]
[HT: Ed Brayton]
apalazzo | November 27, 2006I woke up from a nice restful weekend (the first in a while), to read this crap in today's NY Times. In reference to Dawkins', Dennet's and Harris' books, Richard A. Shweder writes:
...the current counterattack on religion cloaks a renewed and intense anxiety within secular society that it is not the story of religion but rather the story of the Enlightenment that may be more illusory than real.
...
Unfortunately, as a theory of history, that story has had a predictive utility of approximately zero. At the turn of the millennium it was pretty hard not to notice that the 20th century was…
apalazzo | November 26, 2006I heard about this great new (parody) company, NEXTgencode. You gotta love their tagline: Your Destiny is no Longer in Question.
From their website:
Want to see some of their "products"? Here's an add:
And here's even more adds!
Some products include:
- Permapuppy ... have a pet that never grows up!
- Special gene purchases (2XE4 to improve mathematical ability, BLSHt for better verbal facility)
- EnlargeEar ... make your ears 20% larger to "bring you back into the conversation".
(It's funny, while surfing the site we found a link to this other great site.)
For more visit NEXTgencode!
[HT…
apalazzo | November 26, 2006Thursday, my wife and I hosted our annual Thanksgiving for the left behind. Every year, we gather all the foreigners and Americans who couldn't make it back to their own family and have a great big feast. This year, we stuffed 14 people into our small apartment and had a ball. This is the 7th year we've held our left behind Thanksgiving, and since my wife's brother and his wife moved to Boston we had family over as well.
We've been slowly recovering from the big party. It took about a day and a half to prepare the meal, and after the event it took another day to clean the place and an…
apalazzo | November 24, 2006So another week has flown by.
Here is today's mystery campus:
hint: Turkey, what a fine bird.
Leave your answers in the comments section.
apalazzo | November 23, 2006If you haven't seen this, Orac is shocked that I'm shocked and then proceeds to give a run down of other autism related quackery ... go check it out.
In contrast, Abel Pharmboy is joyous about my shockingly shocked post.
OK time to start Thanksgiving day cooking ... oddly enough I'm preparing duck soup as I write this ...
apalazzo | November 21, 2006Autism seems to keep popping up everywhere.
In today's NYTimes there's an commentary on new Federal legislation whose aim is to boost Autism research. But that's not what I want to talk about.
So I've been perusing a couple of blogs by autism researchers to discover that there is a thriving pseudoscience of Autism. For more on this visit BC's blog (Bartholomew Cubbins on Autism). And I know you've probably heard of the heavy metals fanatics (i.e. mercury in vaccines causes autism), but it's worse than that.
Just follow this scary slippery slope of the ill-informed.
So lets say that you buy…
apalazzo | November 20, 2006So not only is McGill's radio station CKUT hosting a new show on global health, Health on Earth, but for their first edition they'll be talking about the Access to Essential Medicines campaign spearheaded by Doctors Without Borders. You may recall that I recently wrote about the student branch of this organization, Universities Allied for Essential Medicines (UAEM). The goal of UAEM is to get their local universities to sign Equitable Access Licenses (EAL) that would lift patent barriers on drugs developed by these institutions. EAL agreements would effectively increase the access of…
apalazzo | November 20, 2006It looks like Tonegawa stepped down as head of MIT's Picower Institute after the kerfuffle over his emails to Alla Karpova, who was offered a job at MIT's McGovern Institute. Read the article in today's Boston Globe: MIT neuroscience center head quits.
On the one hand those emails, although PC on the surface, were pretty nasty between the lines.
On the other hand I've heard that despite his public persona, he's really a nice guy (according to his lab members).
[HT: Zuska.]
apalazzo | November 20, 2006For biologists, this is the magical sentence. N=3. What does it mean?
Well lets say you perform an experiment. You want to see whether protein A binds to protein B. So you run to the lab, pipette away until the wee hours of the morning, prepare a sample, separate your proteins on a gel, probe for the proteins in question ... and you demonstrate that when you isolate protein A, protein B comes along for the ride. As a control, you perform the same experiment without protein A ... and sure enough there is no protein B in the isolated product. Great! But is it true? Perhaps you spit in your…
apalazzo | November 20, 2006In my work, I've investigated mRNA distribution in cells. Many aspects of mRNA metabolism and regulation seem dependent on splicing. And so I've been doing some digging with respect to the survey of intronless genes that I wrote about yesterday. According to their bioinformatic analysis of the human genome, there are over 3000 coding genes that do not contain introns. Here's a comment on this survey from RPM:
From the website you link to:
1. Single exon genes are identified using the CDS FEATURE definition in the genome data.
It seems like they're ignoring introns located in the 5' and 3'…
apalazzo | November 19, 2006Introns are parts of the gene that do not contain coding information, they have to be spliced out of precursor RNA to form mature messenger RNA (mRNAs). But ask most biologists and they'll tell you that in "higher eukaryotes" all genes have introns. All? They may reply, "well not quite". The most famous examples of intronless genes are the histone genes. Also many tRNA genes are intronless. But just how many intronless genes are there in the human genome? Well I just stumbled onto this site: Genome SEGE - Intronless Genes in Eukaryotes.
Here's a couple of graphs from the SEGE (Single Exonic…
apalazzo | November 19, 2006You've probably heard this, but earlier this week many individuals (Shiites, Sunni Arabs, and Sunni Kurds) affiliated with Iraq's small academia were rounded up by gunmen. From the Boston Globe:
On Tuesday, gunmen dressed like Interior Ministry commandos abducted as many as 150 men from the central Baghdad office that handles academic grants and exchanges. The men were handcuffed and driven away in about 20 pickup trucks. About half were released in the next two days.
A Sunni who said he was among the hostages freed asserted the kidnappers broke his arm. He said he saw them kill at least…
apalazzo | November 17, 2006It's been a while since I've written about mRNA and mRNA export. There has been lots of CPEB papers (cytoplasmic polyadenylation element binding protein), but nothing fundamentally new at the molecular level. As for mRNA export, the Reed lab will have a big paper out soon, and when that comes out I'll write a blog about how each step of mRNA metabolism is thought to promote the next step in mRNA metabolism (so that mRNA transcription promotes splicing which in turn promotes nuclear export.)
But for now lets turn our attention to a new JCB paper that claims that a subset of mRNAs, which…
apalazzo | November 17, 2006To quote an ex-Canadian (Jim Carey):
I've [been fixated on] the number 23 for years. It's everywhere. Each parent passes on 23 chromosomes; Earth's axis is at a 23° angle. Psalm 23 is my mantra...
Now he's in a movie called The Number 23 (it's plot sounds almost like Darren Aronofsky's Pi). Here is something else that I read this week in Time Magazine about the movie:
Life has been known to imitate art, as it did on the set of the psychological thriller The Number 23. JIM CARREY plays a man who sees No. 23 everywhere after he starts reading a murder mystery with a plot alarmingly parallel to…
apalazzo | November 16, 2006A couple of weeks back I wrote about dynamins and mitochondrial fusion. Well the latest piece of the puzzle came in ... I just saw a paper in the latest issue of Nature Cell Biology on this very topic. Apparently a mitochondrial version of phospholipase D (MitoPLD) may act downstream of the dynamin like molecule Mfn1 to promote fusion of the outer mitochondrial membrane.
Now remember mitos have two membranes. If two mitos want to get together they must fuse the outer membranes. This requires a dynamin protein (Mfn1 in mammals). After this fusion the two inner mitochondrial membranes can come…