October 10th, 2008 ecoli
story here
A necropsy revealed that a virgin shark was pregnant at the time of death and was nearly ready to give birth. Parthenogenesis was not thought to be common among sharks, the last documented case was at an Omaha zoo in 2002.
Genetic testing confirmed that the unborn shark had no father. The testing was done at Stony Brook University (always like giving a shoutout to my uni) at the Institute for Ocean Conservation Science. This could indicate that parthenogenesis could be more common in sharks than previously thought.
Posted in environment, genetics, link out | 1 Comment »
June 25th, 2008 ecoli
DaveScot, an IDiologist who writes for the uncommondescent blog has claimed to have found a mistake in Richard Lenski’s paper. (which I first talked about here)
He points to a statement made by Lenski: (DaveScot’s emphasis)
However, selection requires heritable variation
generated by random mutation, and even beneficial mutations
may be lost by random drift.
And then points to a study done by the Scripps institute that would seem to contradict this statement:
The bold portion is patently wrong. Selection operates on any heritable variation whether random or not… The Scripps researchers, in a nutshell, discovered that E. coli, when stressed (such as running out of food as in Lenski’s experiment or in the presence of antibiotics in the Scripps experiment) selectively increases the mutation rate on certain genes.
What DaveScot has wrong (and I believe he was refering to this experiment) is that the study says that mutations are purposefully induced on specific genes. However, the doesn’t say that only beneficial mutations are induced or that mutations were localized only to specific genes. This is a case of an organism increasing the rate of random mutations, which is a good survival strategy for a population to increase its genetic diversity. However, it does not appear to be the case, that the bacteria is select for their own survival.
So DaveScot is wrong in saying:
Thus the mutations in this case are not random but rather directed at a certain area in an attempt to solve a certain problem.
There is no basis to this teleological statement. Bacteria aren’t attempting to solve a problem, not in the same humans do when we create a new medicine or drug. They are simply increasing their genetic diversity (and probably not on purpose either, more likely in response to selection pressures), so that when antibiotics are around, the probability of a random mutation conferring antibiotic resistance is increased.
DaveScot FAIL
Posted in creationism, evolution, genetics, link out, microbiology | 9 Comments »
June 10th, 2008 ecoli
The scientists behind Dolly, the world’s first cloned sheep, have been announced as the winners of the Shaw Prize, the million-dollar award known as the Nobel Prize of the east.
Work worthy of a prize, to be sure. But, I find the name of the Shaw Prize a little confusing. Aren’t ’scientists of the East’ already eligible for the Nobel prize? Or is it just that its awarded from the east?
via the Australian Broadcasting Company
Posted in genetics, news | No Comments »
May 31st, 2008 ecoli
Here’s a neat site for those of you who, like me, use Escherichia coli as a model for research. It appears to be a search portal for all things E. coli related, including a genebank and a wiki. I’ll certainly be making use of it in the future.
Thanks to Carl Zimmer at The Loom for the plug.
Posted in genetics, link out, microbiology | 1 Comment »
May 27th, 2008 ecoli
A few days ago, I blogged about a company that put a wide range of long-lasting antimicrobial products into a wide range of products. I wrote the company to complain about their practices, especially in regards to the evolution of antimicrobial resistance, due to the overuse of antimicrobial products.
To my surprise, I actually got a response from Microban International, Ltd. to the email I sent:
Dear Mr. [ecoli]
I appreciate your concern, and applaud your going to the effort of expressing an opinion on an major issue; but I also must point out that this issue shows the need for applying critical thinking to what is published, particularly on science and health in the mass media, and to be sure that you study primary sources of information before forming your opinions.
Resistant strains, such as MRSA, are an issue in the medical use of antibiotics, a subset of antimicrobials with particular modes of action and patterns of use. Microban uses general purpose biocides, another subset of antimicrobials, with multiple modes of action, which do not cause resistant strains as demonstrated in both clinical studies and in over a century of use. Triclosan is one of the antimicrobials that we use, is probably one of the most studied of the antimicrobials, and despite all of the hysteria around it has been shown in something like 6-7 clinical studies, including one by the guy who started the whole thing, and 30 years of use to not cause resistant strains. In addition, our mode of use of antimicrobials, incorporating them into products so that there is always a greater than inhibitory concentration of antimicrobial available, would minimize the likelihood of development of resistant strains; whereas the use of disinfectants and general purpose antimicrobials, common in medical, public spaces, and the home, continually cycles through substantial periods of sub-inhibitory concentrations, a situation far more likely to result in resistant strains but doesn’t. The focus on triclosan and other general purpose antimicrobials is just a red herring that distracts from the real issues concerning the use of antibiotics.
I have attached a white paper that reviews the science behind this issue with regard to general purpose antimicrobials and lists the key papers reporting on the research in this area. I hope that you will take the time to study them.
Sincerely,
Dr. Wayne Swofford
VP, Research & Development
Microban International
I’ve made the paper they gave me available as a Google Doc. I’m going to read the paper in detail over the next several days, but I’m sure at least some of the technical aspects are going to be above my head. So I appeal to the masses to give me a hand in reviewing the paper, to attempt to falsify their work. I don’t want Microban to win out in a simple ‘Appeal to Authority’ if their study is, in fact, bunk.
I urge people who are interested in this issue, to take part. I’ve posted a thread at ScienceForums.net (my home base), which anyone can and should take part in. And, bloggers, feel free to write about this in your own blogs.
Posted in education, evolution, genetics, medicine, microbiology | No Comments »
May 22nd, 2008 ecoli
This blog post is my entry for Skull’s in the stars’s challenge.
- Beadle and Tatum, 1941
About 15 years before Watson and Crick proposed a model for DNA and back when scientists were in disagreement about how genetic information was actually stored, there was the Beadle and Tatum experiment. 
In 1941, American geneticists George Beadle and Edward Tatum, at Stanford University, rediscovered the ideas of the British physician, Archibald Garrod; who, in 1909, proposed that a single gene was responsible for the production of a single protein. Garrod was studying an inherited disease known as alkaptonuria, the production of red colored urine due to an enzyme deficiency.
Based on this work, which had gone largely ignored until then, Beadle and Tatum proposed that, if the “one gene, one enzyme” hypothesis is true, they should be able to produce mutant organisms (in this case the bread mold, Neurospora crassa) with a single gene mutation, corresponding to a single defunct enzyme.
Keep in mind, this is before DNA and cloning experiments and long scientists knew how to produce specific genetic knockouts. Beadle and Tatum, therefore, had to induce non-specific mutations with x-ray and UV radiation. But, by controlling the growth media of the Neurospora, they were able to identify single mutations in biochemical pathways of amino acid synthesis.
Mutated Neurospora was grown in a medium containing all 20 biological amino acids, and the mutated spores were subsequently crossed with wild type spores. Next, the next generation of spores were grown in a medium containing one one of the essential amino acids. If, for example, there was a mutation in a protein that synthesized proline, then the spore would only grow if proline was in the medium (For more background information on amino acid biosynthesis pathways, this is a good resource). Using this method, they were able to link the mutation of a specific gene (which was demonstrated in 1926 by Hermann Joseph Muller) the disfunction of an enzyme related to the synthesis of a specific amino acid.
As in interesting side note to the overall purpose of the experiment, was that they discovered a way by which they could determine the complexity of a specific pathway, by describing pivotal genes, and their enzymes:
in addition to minimal media controlling just the amino acid content, other vitamins and nutrients where also controlled, vitamin B6, for example they realized they could use their technique in a different way. This was a method which they could use to discover entire new pathways, discovering what vitamins and nutrients are essential to growth, and what pathways they are involved in:
The Beadle and Tatum experiment was later revised to include all classes of polypeptides, and not just enzymes, into the “one gene” idea. But, it was their work that was seminal in providing a to link the fields of biochemistry and genetics, providing a way to look at biochemical pathways and protein enzymes through the lens of genetic information, paving the way for later scientists like Watson and Crick, and many others.
Beadle and Tatum shared a Noble Prize in Medicine or Physiology (1958) for their work. A copy of their original paper can be viewed here, I believe for free.
Posted in biochemistry, genetics, microbiology, musings | 2 Comments »
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