The latest issue of Tangled Bank has been published on Evolved and Rational [The Tangled Bank #115: The awesome level is over 9000!].Welcome to the 115th edition of the Tangled Bank, a biweekly blog carnival featuring the best science and medicine posts in the blogosphere. The name of this carnival was taken from Charles Darwin's famous metaphor:"It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us."If you are new to Evolved and Rational, this blog deals with science, evolution, creationism, skepticism, atheism, and internet culture; albeit with a generous serving of lulz. If you like what you see, please subscribe to the RSS feed.
Send an email message to host@tangledbank.net if you want to submit an article to Tangled Bank. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger.
[Hat Tip: Friendly Atheist]
A model organism is one that is amenable to a variety of studies. It often means that it has a well established genetics and that it is relatively easy to maintain in the laboratory. 
"for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid"
Severo Ochoa (1905 -1993 ) received the Nobel Prize in Physiology or Medicine for his discovery of an enzyme that synthesizes RNA from ribonucleotide triphosphates. The enzyme, polynucleotide phosphorylase [Monday's Molecule #90], was first isolated from the bacterium Azotobacter vinelandii. At the time it was thought to be the enzyme responsible for the synthesis of RNA in cells as described in the excerpt from the presentation speech below from the Nobel Prize website [1959 Presentation Speech]. Ochoa's enzyme produces ribonucleic acids from ribonucleotides having twice the ratio of phosphoric acid residues as that contained in ribonucleic acid. The ribonucleic acid is formed by splitting out half of the phosphoric acid residues, and linking the nucleotides together to form large molecules, which, as far as we can prove today, do not differ in any way from natural nucleic acids. Kornberg's enzyme produces deoxyribonucleic acids in a similar, but not identical fashion. Both have arrived at the same, principally important result that in order to make the reaction start, it is necessary to add in the beginning a small amount of nucleic acid to act as a template. Otherwise the enzymes do not «know» which kind of nucleic acid they are to produce. As soon as they get a template to act as a guide, they start, just like a skilled type-setter, to copy the «manuscript» they have received. Here one recognizes life's own principle that like creates like. Even though several research workers had earlier suspected that such a mechanism was involved, the actual experimental proof is of greatest importance. Furthermore, Ochoa's enzyme has given us the possibility of enzymatically synthesizing simplified nucleic acids of great interestWithin a short time, scientists began to realize that polynucleotide phosphorylase did not require a DNA template. The enzyme synthesized random polymers of ribonucleotides in a reaction that is now recognized as a way of salvaging RNA in bacterial cells.
Within a few years Marshall Nirenberg, Gobind Khorana, and others began to exploit this enzyme to synthesize synthetic RNAs that were used to crack the genetic code [Nobel Laureates: Robert W. Holley, Har Gobind Khorana, and Marshall W. Nirenberg]. To celebrate his 70th birthday in 1975, Ochoa chose as guests the scientists he most respected worldwide. Symposia and celebratory dinners, starting in Barcelona, were followed by a visit with Salvador Dali in his museum in his hometown in Figueras and culminated in a gala of events in Madrid. It was a party, the likes of which has not been seen in scientific circles before or since.
[Photo Credits: Top: Kornberg (2001), Bottom: Severo Ochoa: La Conquista del Nobel]
Kornberg, A. (2001) Remembering Our Teachers. J. Biol. Chem. 276:3-11. [JBC Online]
When you get to my age, more and more of your female relatives, friends, and acquaintances will be diagnosed with breast cancer. They will be undergoing more or less radical surgery followed by chemotherapy and/or drug treatment. One of the most common drugs for the treatment of breast cancer is tamoxifen.1. This isn't quite true. Tamoxifen itself doesn't bind to the estradiol receptor protein, instead it is converted inside your body to other chemicals that do bind.
Yamamoto KR, Alberts BM. 1972 In vitro conversion of estradiol-receptor protein to its nuclear form: dependence on hormone and DNA. Proc. Natl. Acad. Sci. USA. 69:2105-2109. [PubMed]
I know, I know. Beating up on PETA is like beating up on a helpless puppy dog, except that puppy dogs are cute and lovable, and PETA is anything but either of the two. It's also too damned easy, leaving me feeling vaguely guilty when I'm done for not going after a more challenging target. I do it anyway because the level of sheer irrationality demonstrated by PETA with each and every one of its campaigns just irritates the hell out of me. I hate having my intelligence insulted in such a manner. Also, the sheer publicity whoring for which PETA is so well known irritates me. It's painfully obvious that PETA doesn't give a rodent's posterior about helping autistic children. It just knows that autism has been in the news a lot lately and decided a good way to get publicity would be to latch onto autism somehow, no matter how tenuous the link they come up with to justify their billboard. Not that it will matter to most PETA supporters or to the "biomedical:" (translation: antivaccinationist) movement. Indeed, this latest campaign is so idiotic that I almost expect to see it touted on autism quackery websites soon.
There, now. I feel better. Slapping down PETA is always a fine diversion when my workload gets too heavy and I need a break. Hopefully, I can pick a more challenging target next time. On the other hand, so much woo is no better than this; so I'm not sure there really is a much more challenging target in that realm.
Read the list of blogger nominees from last year and the year before on The Daily Transcript. I'm sticking with Ernest McCulloch and James Till (see photo) for the discovery of stem cells.
Today is the day Canada's DO NOT CALL (DNCL) list comes into effect. If you register your phone number with the Canadian Radio-television and Telecommunications Commission, telemarketers will not be allowed to call you without breaking the law ($15,000 fine).There are certain kinds of telemarketing calls and faxes that are exempt from the National DNCL, including those made by or on behalf of:The new legislation that comes into effect today stipulates how telemarketers are supposed to behave when you are called.Telemarketers making exempt calls must maintain their own do not call lists. If you do not want to be called by these telemarketers, you can ask to be put on their do not call lists. They are obliged to do so within 31 days.
- registered charities seeking donations
- newspapers looking for subscriptions
- political parties and their candidates, and
- companies with whom you have an existing commercial relationship; for example, if you have done business with a company in the previous 18 months––such as a carpet-cleaning company––that company can call you
Among other things, telemarketers must:You can put your phone number on the list at DNCL or by calling the toll-free numbers 1-866-580-DNCL (1-866-580-3625) or 1-888-DNCL-TTY (1-888-362-5889).Telemarketers must not use Automatic Dialing and Announcing Device (devices that dial telephone numbers automatically and deliver a pre-recorded message). However, these devices can be used by police and fire departments, schools and hospitals, as well as for appointment reminders and thank you calls.
- identify who they are and, upon request, provide you with a fax or telephone number where you can speak to someone about the telemarketing call
- display the telephone number that they are calling from or that you can call to reach them, and
- only call or send faxes between 9:00 a.m. and 9:30 p.m. on weekdays and between 10:00 a.m. and 6:00 p.m. on weekends
Identify this molecule. You need to describe what you see as accurately as possible and name the species from which this protein was purified. I don't think any of you can do it without a hint so here's a clue.11. It is NOT the flying spaghetti monster. GSSGSSGPQKIFTPSAEIVK YTKIIAMEKLYAVFTDYEHD KVSRDEAVNKIRLDTEEHLK EKFPEVDQFEIIESFNIVAK EVFRSIILNEYKRCDGRDSG PSSG
I probably need to explain strategic voting to those people who don't have the "advantage" of living in a multiparty democracy. Strategic voting is where you deliberately vote for someone who is not your first choice in order to prevent another candidate from winning in your riding.
My name is Jennifer, and I support strategic voting.I know other people who are going to hold their nose and vote Liberal even though they are dissatisfied with the Liberal Party and with their leader Stéphane Dion. They realize that by switching their vote to the NDP, Bloc, or Green Party, they will make it more likely that Stephen Harper could remain Primie Minister with a majority government.
1. Everyone with an I.Q. over 50 realizes that we need to change our voting system from first-past-the-post to some sort of proportional system. But that's not going to happen for many years. First, a lot of stupid people have to die. Meanwhile, we're stuck with the debate over strategic voting.
Nils Reinton is a molecular biologist working in the field of medical diagnostics and he has been challenging the concept of junk DNA in the comment section of a recent posting. The title of that posting, Everything Is There for a Reason?, was direct response to an earlier posting from Nils where he claimed that we shouldn't label DNA as "junk" because it's a science stopper.Q: Why is the Fugu genome so much smaller than that of other fish?No, my argument was not that the extra DNA has to be junk just because there are two similar species that differ in the sizes of their genomes.
and
Q: When two similar species differ in genome size by a factor of two—probably due to an ancient polyploidization—is the majority of DNA in both species functional?
A: His argument is that since the genome size differs between species, much of it must be junk. But, you could easily use the same argument towards a function, by saying that the difference in genome size is a defining (functional) difference between species. We just do not know do we ! And, why does the difference in size not give you reason to speculate on function at least in parts of these regions ? Others have however, speculated far better than me on this topic, and a thorough introduction to such research can be found at junkdna.com and following this link to “The Principle of Recursive Genome Function“.
Q: In the human lineage there are over one million Alu sequences. They all look like degenerate versions of 7SL RNA. Are all of these sequences functional? If so, what function could they be doing? And why do the human Alus look so different from the mouse ones?My position is that a huge amount of the DNA in our genomes is junk. That position is based on many different lines of evidence as well as on rational extrapolation from what we know and don't know about molecular biology and evolution.
A: I am not saying all Alu-elements are functional. On the “what is junk” scale, one extreme is that everything that hasn’t been ascribed a function is junk (Larry Moran’s position !?) and on the other end is “nothing is junk”. My position is somewhere in the middle: Some of the DNA in our genome is possibly junk. A number of individual Alu-elements will undoubtedly end up in the “junk”-category when more is known about our genome. That said, it has been shown that Alu-elements can constitute (parts of) regulatory and functional elements. It’s rather hard to tell which ones are functional by just looking at them. I therefore refuse to call them “junk” by default, - I strongly feel that the “junk”-label is a dismissal of any possible function(s) and should be used with caution if at all, - even for Alu-elements.
Q: Most intron sequences do not seem to have a function. Why does the size of introns in the same gene vary so much in related species and why isn’t the sequence conserved in most cases?The fact that we have a few examples of functional intron sequences is no reason to assume that most of them are functional in the face of abundant evidence that they are not. That's a position that only a confirmed adaptationist would take.
A: This argument is similar to the genome size argument above, and the answers for bullet 5 and 6 are equally valid here. Thus, there may be many reasons for a variation in intron size and this variation is not a very good argument to support the “junk” hypothesis. Also, the intron can contain regulatory elements and the c-gamma example above goes to show that introns can even contain functional (as in transcribed) genetic elements.
