Archive for category Science

Beautiful proteins

I started a new blog: http://beautifulproteins.blogspot.com/ . For a while now i’ve been collection PDBs of proteins that i come opon through my work that i find beautiful for some reason. I’ve decided to post some of them to a blog called Beautiful Proteins. Example: Neurotrophin (NGF, Nerve Growth Factor):

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100 Most Frequent Internet Search Terms

I’ve been tinkering around, trying to find out what are the most popular searchterms typed into google these days ? Google Trends offers a wealth of data, as do other sites and Meta crawlers and analysis sites. Most published analyses omit adult terms while others (such as Zeitgeist published by Google) concentrate on terms whose search volume is rising quickly compared to their long-term average volume. I feel its insightful to also look at more absolute values though. So here’s a list of the most popular terms I could find: (note this list is approximate and not necessarily complete, nor is the ordering super accurate. The first 10 are fairly accurate though.)

  1. Facebook
  2. Free
  3. How to
  4. YouTube
  5. Online
  6. Lyrics
  7. New
  8. Download
  9. Games
  10. Yahoo
  11. Google
  12. My
  13. School
  14. Porn
  15. Uk
  16. News
  17. Best
  18. Weather
  19. Mail
  20. Sex
  21. Hotmail
  22. Movie
  23. Video
  24. Bank
  25. City
  1. Bank
  2. Ebay
  3. University
  4. Game
  5. Tv
  6. Facebook login
  7. At
  8. 3
  9. Home
  10. MySpace
  11. Time
  12. Map
  13. Car
  14. Music
  15. Movies
  16. College
  17. Jobs
  18. BBC
  19. Club
  20. Up
  21. Park
  22. State
  23. Code
  24. House
  25. Hotel
  1. IT
  2. Canada
  3. Craigslist
  4. Free download
  5. House
  6. Hotel
  7. Black
  8. Yahoo Mail
  9. Girls
  10. Wiki
  11. Love
  12. American
  13. India
  14. Watch
  15. Live
  16. Gmail
  17. White
  18. Book
  19. Office
  20. Football
  21. Videos
  22. Song
  23. Big
  24. CA
  25. Song
  1. Top
  2. London
  3. Hot
  4. Girl
  5. Life
  6. Blue
  7. MSN
  8. Radio
  9. Star
  10. Real
  11. Recipe
  12. You Tube
  13. Texas
  14. Card
  15. Baby
  16. Store
  17. Sports
  18. Health
  19. Australia
  20. Software

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Good Science

This interesting editorial published in Nature (reproduced below without permission) below illustrates a sad truth in the world of science. Since everyone is under huge  political and financial pressure to publish, perform and be the first (the price for second discoveries are already muchly reduced), there is a tendency to over sell and overhype results, publish quickly before the results are properly confirmed and to claim “XYZ is solved” when really it barely worked for one out of 100 cases. Another case is that of Prof Helinga in the field of enzyme design (the results of his groundbreaking enzyme design study were withdrawn, sicne they could not be reproduced, read more about it here ).

I suspect that these cases occur not out of malicious misconduct or out of want for success or ego (i think they partly do though) but largely out of political, social and financial pressure. This does of course not excuse bad science but it raises the question on how to improve the quality of scientific conduct, results and publication. There is a fine line between needing to publish quickly to be the first and scientific rigor. Between boldness and negligence.

Editorial

Nature 461, 1174 (29 October 2009)

Mind the spin

Scientists — and their institutions — should resist the ever-present temptation to hype their results.

The circumstances surrounding the recent announcement of results from an HIV vaccine trial in Thailand are troubling. The sponsors of the US$119-million phase III clinical trial, a consortium led by the US Army, the National Institutes of Health and the Thai government, announced on 24 September that the trial had been a success: an analysis of the data showed that the vaccine had a statistically significant effect on preventing infection.

Other scientists could not immediately assess that claim, however: the full data from the trial were not made available until 20 October, when they were presented at an AIDS vaccine conference in Paris and in an article published online the same day (S. Rerks-Ngarm et al. N. Engl. J. Med. doi:10.1056/nejmoa0908492; 2009). The article contained two other data analyses, not mentioned in the initial announcement, showing smaller effects that were not statistically significant (see page 1187).

The trial’s sponsors defend the premature announcement on the grounds that they had promised to inform the Thai people of the results first; 24 September is also Mahidol Day, the anniversary of the death of the king’s father and a day of national observance in Thailand. The sponsors also argue that announcing the less-upbeat analyses along with the positive result would have been too complicated for the public to understand; they wanted to quickly deliver a clear-cut message on the trial’s findings. Making the full data immediately available to scientists on 24 September would also have been impossible, they add, because of the conference and journal embargoes.

The trial sponsors argue that announcing the less-upbeat analyses along with the positive result would have been too complicated for the public to understand.

To their credit, the scientists involved did emphasize in their public statements that any vaccine effect was “modest”, and that the vaccine itself was of no immediate public-health utility. At the same time, however, they hammered home the message that this was “the first time an HIV vaccine has successfully prevented HIV infection in humans”, and implied that the event was somehow historic. Such statements, together with the selective initial presentation of the data, are well outside the scientific norms for presenting the results of clinical trials. They inevitably create suspicion that the trial sponsors may have put an excessively positive spin on results that are far from clear-cut, in a trial that has long been controversial (T. V. Padma Nature Med. 10, 1267; 2004). The trial has also been six years in the works, and so there seems no particular public-health urgency to justify publication by press conference.

Fortunately, such stories are still rare in science. Witness the way scientists have behaved since the beginning of the current H1N1 flu pandemic, in which the urgent threat to health creates legitimate tensions between getting results out fast and respecting peer review. Most researchers have negotiated this tension well, through a combination of fast-track publication by journals and online pre-publication sharing of preliminary data — but not through hyping their results.

Yet the temptation for scientists and their institutions to spin their research to the media, or to go publicity-mongering, is always there. And — as illustrated by the excessive public-relations campaign surrounding Ida, a fossil presented as a missing link in human evolution (see Nature 459, 484; 2009 and Nature 461, 1040; 2009) — too many in the media will buy into the initial hype.

Such behaviour is corrosive to the process of scholarly scientific communication. Research institutions must not allow it to become the norm.

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Cassini Mission – The first 1000 days

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My first talk at Ignite !

Last week I talked at Ignite 7 in Seattle about the rotation mechanism of F0F1 ATP-Synthase . I love Ignite and was hoping to be able to give a talk at one ever since I’ve been to one. Sharing something you’re excited about is really fun and exciting and the format at Ignite is a wonderful way to find out about things far outside your expertise without getting bogged down in the the nitty gritty details.

http://www.igniteseattle.com/2009/07/the-invention-of-the-wheel-mike-tyka/

Here are the slides:

http://www.miketyka.com/data/MikeTyka_InventionOfTheWheel.ppt

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