Wednesday, October 05, 2005

Tangled Bank #38

Welcome to Tangled Bank, Issue 38! It is a great pleasure to bring this edition to you, which has 41 fabulous contributions (if I counted correctly), so there is something here for everyone. Regular readers will notice that there are quite a few women, "non-Americans" and first-time contributors, which pleases me greatly. I hope they all continue to contribute to future editions of Tangled Bank. You can help in this endeavor, dear readers, by making useful or encouraging comments on their essays. After all, we write for you, and we love to hear from you!

You will also notice that there are a few nominations to this issue, and I thank those who helped me by sending links to these essays and blogs. I hope to notify those authors of their special "nomination status" very soon via email.

I would also like to say that I did not accept all submissions. I apologize for this, but I had a difficult time trying to fit every essay in with the topic format that was developing. Feel free to resubmit to the next Tangled Bank host.


Evolution and Defining Science


PZ Myers, the father of Tangled Bank and the author of Pharyngula, sent this wonderful contribution, “Tales of the X-Mice: how to regenerate”. In this, PZ's review of an interesting scientific paper by Heber-Katz and colleagues, he writes; an evolutionary lesson from this animal is that it represents a more likely example of how advantageous novelties arise: not by abrupt transformations of single genes, but by fortuitous recombination of smaller, hardly noticeable variants that, when they come together in a single individual, interact to produce a new phenotype.

Steve Reuland, a biochemist and contributor to The Panda's Thumb, submitted his essay that describes the "holy grail of biochemistry", solving the “protein folding problem“. Simply stated, "the protein-folding problem" refers to the mystery surrounding the mechanics of how a linear chain of amino acids can fold up into a properly functional three-dimensional shape (an incorrect 3-D shape alters the protein's function). Steve reviews two scientific papers that reveal how statistics that are used in evolutionary analyses are also useful for determining the shape of a mature protein. Steve's conclusion; the seeming difficulty with which proteins fold has at times been used to argue that new folds could never evolve, or that protein folds could never have arisen de novo. These claims are similar to the type that William Dembski has made about protein function, which doesn’t stand up well to scrutiny. But such arguments are always easier to sell when applied to things we know little about, like the protein folding problem, since one can always appeal to “high information” content and whatnot to say that protein folds could never evolve. Unless, of course, it turns out that they don’t require high information content.

How can the world's smallest birds survive the coldest of nights when they cannot forage for food? In this story-essay, written by me, your humble host, I describe how torpor is an evolutionary adaptation used by hummingbirds to survive cold nights. The story includes an interview with a graduate school colleague of mine who is a hummingbird expert. I hope that you enjoy it.

Dave Thomas from The Panda's Thumb nominated this delightful and intelligent essay that is part travelogue, part teamwork and all about evolution, “Steve Steve and the Fossil-Fossils of De-Na-Zin.” Professor (Steve Steve) Panda's essay discusses the so-called fossil-fossils of trilobites and bryozoans, and the evidence of prehistoric floods that blow “creationist flood geology right out of the water.” This essay also has lots of great pictures of the adventure.

I found (and nominated) this essay describing one aspect of the evolution-creationism debate during my wanderings through the blogosphere, and thought you might also enjoy reading it. Thompson Shows Why ID is not Falsifiable. This is so important because one of the primary distinctions between science and religion is whether a hypothesis or theory can be falsified when an inconsistent set of data are found. The author is Ed Brayton, a freelance writer, author of the blog, Dispatches from the Culture Wars, and a partner in a mortgage company and a political consulting firm. The comments following this essay are also quite interesting.

In Understanding Evolution, Martin reviews the University of California, Berkeley's a new website and describes his misgivings about the way homology is taught to students. Martin is a graduate student and author of the new blog, The Lancelet.

What does the Theory of Relativity have to do with evolution? The author of the blog, The Questionable Authority, explores this relationship in a story that he published on the 100th anniversary of the fourth paper published by an unknown physicist. These four papers, all controversial and most of them short and elegant, changed theoretical physics forever. Even though this story begins by talking about physics, it notes that one hundred years later, science is again under attack by a group of people who claim they too, have a similarly earth-shaking idea that describes the origin of life. This story details the huge chasm that separates creationists and IDists from scientists. Be sure to read the comments, too.


Medical Research


If you share my morbid fascination with diseases, epidemics and other things microscopic, you'll be enthralled by Night of the Living Dead. This beautifully written essay by DarkSyde, one of the authors at The Daily Kos, is about the history of Black Death, the AIDS pandemic, and the human immune system. Don't forget that humanity represents the largest pile of meat on earth, and enterprising bacteria and viruses are scheming overtime for how they can eat it. All. Also includes pictures.

Mitochondria are tiny "organelles" found in all living animal and plant cells, but mitochondria are unique because they contain their own DNA and can divide independently of the cell they live in. Mitochondrial DNA is essential to the functioning of our cells, but is damaged much more readily than nuclear DNA; this damage is implicated as a cause of a range of age-related degenerative conditions. This short commentary was inspired by Frank Rummel's fascinating blog report that describes progress towards copying mitochondrial genes into the cellular nucleus - this is one proposed strategy for mitigating age-related cellular damage, thereby possibly slowing the aging process in humans. Dr. de Grey says, Rather than fixing mitochondrial mutations, we can obviate them. We can make copies of those 13 genes and put these copies into the chromosomes in the nucleus. Then, if and when the mitochondrial DNA gets mutated so that one or more of the 13 proteins are no longer being synthesized inside the mitochondria, it won't matter -- the mitochondria will be getting the same proteins from the nucleus.

Dr. Hsien Hsien Lei, author of the Genetics and Public Health Blog, contributed this article about cloned mice carrying a complete human chromosome 21, serving as a model for Down's Syndrome. Despite the fact that critics protest that scientists have "violated the boundary between human and animals", Lei counters their argument by saying that having a mouse model in which to study the genetics of Down's syndrome would be an invaluable way to understand which specific genes increase the risk of medical conditions which are prevalent among people with Down's syndrome: impaired brain development, heart defects, behavioral abnormalities, Alzheimer's disease and leukemia.


Medicine


Cary contributed this amazing short story about his new wife, Lori, for you to read, Congratulations on Your Marriage, Your Wife Has a Few Months to Live. Cary publishes the Cancer Watch blog, that provides updates on the latest cancer news. In my opinion, this story and the one following make an interesting combination.

Speaking of cancer, I nominated this personal story, Within These Hands, written from the oncologist's point of view by The Cheerful Oncologist.

After reading those previous two stories, you might be curious to know if the life of a doctor is full of sadness. It isn't. I also took the liberty of nominating this odd short story, The City That Never Sleeps for your reading pleasure.


Ecology, Environment and Conservation


In this long but eloquent essay written by my friend, Chris Clarke, author of the beautifully-written blog, Creek Running North and editor of the Earth Island Journal, describes how ten thousand years of history were changed with the introduction of a handful of invasive plant species into the Mojave and Sonoran Deserts of the Southwestern United States. In this essay, Chris describes the aftermath of the Hackberry Fire in the Mojave National Preserve in Arizona. He then focuses on one invasive alien species, Buffelgrass, Pennisetum ciliare, and goes on to discuss the complexity of the desert ecosystem, how it changed and reveals that there might not be any solutions to this tragic loss.

Mike at 10000 Birds contributed this brief piece that describes the ecology of a travesty, an interesting point-by-point overview of the human-induced effects that are making life very uncomfortable and increasingly untenable for most other animals on the planet.

Daniel, author of A Concerned Scientist, contributed this analysis that should be required reading for George Bush and cronies, showing that the ESA works, and isn't a threat to landowners. This piece includes links to previous commentary by Daniel regarding this issue.

Ranger Bob is a retired National Park Ranger who remains concerned about our public lands. In this essay, Parks For Sale, he sounds the warning that legislators are proposing to sell 15% of our public lands and 15 national parks to help with hurricane relief and shore up the national debt. Ranger Bob states that one of these so-called "representatives, Tom Tancredo (R-CO), has no clue that these lands are held in trust for the American People who have a voice in the matter. Which makes me hope that We the People recognize that we do have a voice in this matter and that we use it! Ranger Bob, a first-time contributor to Tangled Bank, is the author of the blog, Neo Commons. Please be sure to make him feel welcome.


Science Education


My pal Orac, a medical doctor and author of Respectful Insolence, is a man after my heart, even though he did commit a small faux pas by not finding the idea for this story from my blog (grr!). This essay comments on the letter that was published in the top-tier scientific journal, Nature, that proposed a genetic system for inheritance of magical powers for the characters in the Harry Potter books. The letter was proposing that Harry Potter could make it easier to teach kids the basics of Genetics. Orac goes on to include a reply to this letter, also published in Nature, that states that magical abilities might instead be only partly inherited, that the allele for magical abilities might only be fully expressed when triggered by some external factor, such as exposure to magic or infection with a particular microbe.

Ronald writes a short description of a classroom method for teaching the concept of evolution in Intelligent Design - Flipping Wrong. Even though he intended to illustrate the nature of the creationists' protests about evolution in this essay, I think it is a wonderful practical way to approach evolution in the classroom, especially when used in conjunction with the "Harry Potter method" of teaching genetics described by Orac (above). Ronald is the author of the blog that bears his name.

Fred recently returned to teaching after burning out on his second career in health care. He wrote this lovely reflection concerning how out of touch with nature our young people have become during the past 17 years. Fred, author of the blog, Fragments from Floyd, is another first-time contributor to Tangled Bank.

Tired of trigonometry? Having trouble keeping track of all those sines, cosines, tangents, cotangents, et cetera, and so on and so forth? Ironman at Political Calculations looks at a new approach to the subject that claims to drastically cut down the amount of time required to learn it in his contribution, rewriting the rules of math.

My blog pal, Bora, is a graduate student and author of Science and Politics, continues to entertain with his dry wit by translating an amusing blog entry, Astrology Academy in Serbia, and the resulting comments from Serbo-Croatian into English.

I consider the reporting of science to fit under the rubric of education, even though it is not a formal education as that presented in schools. Doctor Free-Ride, Ph.D. is a philosopher who was also a chemist at one time, and she also is a first time contributor to TB. In this essay, blueprint to improve science journalism, she comments on an essay by PZ Myers (link included) and discusses the realities of scientific research and science writing/journalism. Her conclusions? Scientists need to help journalists by working out at least a good "cocktail party" explanation of what they’re studying, how they’re studying it, and why it matters. Scientists and science journalists can help the public understand that sometimes we are benefited by simply coming to better understanding of a piece of the world that intrigues us. But, if scientists can’t explain why this matters, no fair blaming the journalists for not explaining it.


The Evolution of a Scientist


This interesting piece, written by an Anonymous Science Student, was nominated to Tangled Bank by Dave, editor for the new online blog and ezine, Science Creative Quarterly. In this essay, The Science/Arts Divide Stands Between Us: A Love Story, Anonymous Science Student (who also is a student of the Arts) reveals that he feels uncomfortable with the arrogance displayed by some students of science and states that there are things that are important in life other than being a scientist.

Long-time TB reader and first-time contributor, Elia Diodati, is a second-year graduate student and the author of the thoughtful blog, e pur si muove (Italian for But it does move -- attributed to Galileo). In this essay, Second Year Blues, she describes feeling overwhelmed with the required second-year coursework for her degree program, stating that one will eventually have to become familiar with a significant portion of the entire sum collection of human knowledge and ingenuity in his or her field of specialization.

This little essay by third-year botany graduate student, BotanicalGirl, was nominated by both Doctor Free-Ride, Ph.D. and me; Science Never Sleeps. It describes the realities of bench research, particularly the inherently high failure rate.

Mike the Mad Biologist, a postdoctoral fellow and author of The Daily Transcript, worried that he sounded too whiney in this essay, The Worst Things About Science. I assured him that he did not, partly because if he sounds whiney, well, I sound even worse. Be sure to read the comments, too!

I nominated this essay written by my blog pal, Ms. PhD. This piece describes the shark-infested waters of dealing with grouchy lab members & lab etiquette. I assume most of you recognize this environment, even if you aren't scientists!

In this essay, nominated by moi, Derek speculates on the age-old question, Where Do the Good Ones Go? Derek is a chemist who works at a pharmaceutical company and who writes the very interesting blog, In the Pipeline, that mostly discusses the "industry of science". To the best of my knowledge, this is the first time that Derek has been listed in an edition of Tangled Bank.


The Poetry of Science


Socar, a misplaced Brit who is a poet and author of the amusing blog, Ratty's Ghost: Observations of a Bewildered Rat, somehow heard of my love for poetry and so obligingly sent in this witty and wonderful contribution around midnight, or perhaps early this morning, when I was busily wondering what happened to my neighbor's wireless connection that I have been er, borrowing. This poem, What Rotten Luck, Old Sock, Old Bean!, is the epic tale of a rat whose winters number three/ An ancient fellow, stiff of knee who plotted to pounce on Death, ere Death pounce him. Socar respectfully requests that you, dear readers, pardon the mention of God but she was stuck for a rhyme!

Guru, a metallurgist with a specialization in computational materials science who lives in Bangalore and writes the blog, Malkanthapuragudi, sent me this brilliant poem parody, modeled after The Rime of the Ancient Mariner (link included for easy comparison), called The Rime of the Ancient Researcher. This parody is described by Guru as the story of how a grad student, having passed the Comprehensive [exam], was driven by experimental difficulties to the desert Country of NoResults; and how from thence she made her course to the warm latitude of the CuriousResults; and of the strange things that befell; and in what manner the Ancyent Researchere came back to her own Doctorate. I am not sure, but I do believe this is Guru's first submission to Tangled Bank, so please make him feel welcome!


Science, Philosophy and Ethics


John has written about a topic that is near and dear to my own feathery heart; Conservative Penguins? He starts out by observing that the summer blockbuster, March of the Penguins has proven popular among conservatives because they see it as supporting their moral and political agenda. Unfortunately, if they actually knew anything about the natural history of penguins, they'd quickly change their opinion. John goes on to point out that it is a bad idea to try to use the animal world as a morality play. We like to see reflections of our own emotions and motivations - dogs are loyal, cats are mischievous, and Antarctic penguins fall in love. .. But there will always be a gap between humans and other animals, and trying to pretend it does not exist is fair neither to humans nor to other creatures, which ought to be understood on their own terms. John is author of A DC Biridng Blog.

Louis, a Canadian, is another first-time contributor to Tangled Bank. In his thoughtful and well-written essay, Art and Science Perverted, he expresses his concern regarding the uses of science, and cautions us that we should be careful that science is never distorted to justify ideological or political pursuits. He observes that in the United States, there is at present the strongest tendency for perversion of science to happen: in reaction to the teaching of evolution, religious fundamentalists are pushing creationist (a.k.a. "intelligent design") ideas under the disguise of “scientific” discourse; or scientific findings about climate change and global warming are discredited or simply ignored in order to preserve the American economy from any disruption. Although he says that some of the references to current events are a bit old, I think the core of the text is important, and should interest you. Louis is the author of Gold Blog Variations.


Other Scientific Fields

    Neurobiology, Cognition and Language


Dave Munger is a professional writer and co-author of the blog, Cognitive Daily, a blog that discusses the scientific literature about human cognition. In this essay, Dave reviews a paper written by Gaunet and colleagues that explores how humans navigate through "feature-rich environments". After describing the details of the experiments, Dave asks; Do we use dead-reckoning, depending on memory for where we've turned and how far we've gone, or do we depend on landmarks to help remember where we've gone?

My blog pal, Joseph, a medical doctor and author of The Corpus Callosum, contributed this piece that he described as "thought-provoking armchair musings that have something to do with natural science". In this essay, he discusses what the placebo effect "looks like" using a PET scan of the brain, and then goes on to wonder if the placebo effect is operating with troubled people who are on wait-lists to see a therapist. I won't spill the beans here about his hypothesis and the evidence that appears to partially support it, but I guarantee that you'll find it fascinating reading.

Mark Rayner contributed this humorous look at the scientific study proposing that swearing is part of all language development, Thag not like f#&*ing shaman!. This story includes a link to the NYTimes article describing the original research. Mark writes the blog, The Skwib.


    Astronomy


Phil, who describes himself as an astronomer, writer and skeptic, is the author of Bad Astronomy Blog. He went to a presentation by a NASA scientist, Chris McKay, and wrote Titan Rocks, an interesting essay that discusses the incredible data gathered by the Huygens space probe sent to Saturn's biggest moon, Titan. Be sure to also read the comments following this essay.

Do you remember the "pet rock" craze of last millennium? Did you really enjoy your "rocks for jocks" class in school? Or perhaps you like drinking McDonald's milkshakes? Well, WolverineTom apparently does, and so he is taking Friday Cat Blogging (dog, bird, invertebrate, plant and what-have-you blogging) to the edge of life by sending this short essay for your reading pleasure, Sunday mineral blogging: Kaolinite.


    Botany


In this short but elegant essay published on the University of British Columbia Botanical Garden blog, Daniel wonders what smells like cow manure from ten meters away, yet only stands 15cm tall? Includes a picture of the little rascal. GrrlScientist note: this rascal looks like a piece of bacon wrapped around a couple blades of grass.


    Archaeology/Economics


Oxford University Press is getting into the blogosphere, too. On their blog, one feature is their authors' answers reader questions about the books they wrote. The Press promises that the 5 readers whose questions are chosen to be answered will each receive a free copy of a book. This contribution, A Return to Prehistory?, is the fourth part of a series of excerpts from a OUP new book called The Fall of Rome And the End of Civilization by Bryan Ward-Perkins. In this essay, the author makes the argument that the end of the Roman world is not a ‘recession’ or – to use a term that has recently been suggested – an ‘abatement’, with an essentially similar economy continuing to work at a reduced pace. Instead, what we see is a remarkable qualitative change, with the disappearance of entire industries and commercial networks. The economy of the post-Roman West is not that of the fourth century reduced in scale, but a very different and far less sophisticated entity.


Miscellaneous Science


This essay, Everything Scientific Vol. II, is a round-up and commentary on some of the most significant scientific findings in the past couple weeks by Sunil, author of the interesting blog, Balancing Life. Sunil is Indian but currently resides in my beloved other home, Seattle. This story includes links to the original research papers.

Rob has been photographing and collecting unusual objects for quite a few years and just recently started posting them on his blog as puzzles for viewers to identify. He contributed this interesting piece for your amusement, what is it? Additionally, he recommended another blog maintained by Walt Anthony that shares optical illusions that you might enjoy.


The Fine Print (Information about the next Tangled Bank):


Thanks so much to the contributors for making this issue of Tangled Bank a success! The next issue of Tangled Bank will be published on 19 October 2005 at The Questionable Authority. Submissions can be sent to PZ or to host at tangled bank.

Tangled Bank is always looking for bloggers to volunteer as hosts, especially beginning in January 2006. If you are interested to host Tangled Bank, please contact PZ so he can add you to the list! If you want to know what hosting a blog carnival such as Tangled Bank entails, you should read this essay where I describe the first time I hosted TB (this is the second time I've hosted TB).

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© 2004, 2005, 2006 by GrrlScientist

17 Peer Reviews:

Blogger coturnix said...

Wow! It is huge! And wonderful!!!!

Isee I will not get anything done today - too much good stuff to read. And several blogs new to me are here that I need to explore more.

Thank you!

12:15 PM  
Blogger Big Fat Rat said...

"...s/he was stuck for a rhyme."

Oops! Pardon my failure to introduce myself, when I sent along my submission. I was so anxious to get it in before the deadline, I completely forgot. My name's Socar Myles. I'm female, British, and currently living in Canada. Pleased to meet you!

Also, lovely job! This is a most overgrown Tangled Bank, indeed--full of interesting weeds and scurrying hoozits. I'm looking forward to reading every last one, later this evening. It's great to see representation from so many corners of the scientific world.

1:15 PM  
Blogger BotanicalGirl said...

I'm thrilled to see I was nominated, as I meant to send you something to include but got very busy and also didn't think I had a worthy entry this week. Glad to see I was wrong.

Excellent job collecting and organizing the Bank this week! I have a billion links to read...

1:39 PM  
Anonymous ctenotrish said...

Soooo much great stuff to read! Thanks for assembling it all. Just one *possible* correction, though. The Mad Scientist post about Worst Things in Science (and I agree with them all, speaking from the writing madly, post procrastination standpoint) comes from what I think is a different person than Mike the Mad Biologist, who's blog I also quite like. See the two urls below. My regrets if they are the same person, or if Mad Mike is a part of the Mad Scientist set-up . . . .

http://ribonucleicacids.blogspot.com/2005/09/worst-things-about-science.html

http://mikethemadbiologist.blogspot.com/

Thanks for the lovely Tangle! Ctenotrish

2:02 PM  
Anonymous ctenotrish said...

oops: 'whose' not who's

2:04 PM  
Anonymous evilchemistry said...

Bacteria and Archea are living cells without mitochondria. Thank you, can't wait to read all this interesting material.

2:18 PM  
Blogger tony g said...

Fantastic piece of work! Congratulations . . .

tony g

2:30 PM  
Blogger GrrlScientist said...

Thanks everyone for spotting my mistakes. I think I have corrected everything ..

GrrlScientist

2:39 PM  
Anonymous Derek Lowe said...

Thanks very much for including me in this edition. Clearly there are more blogs that I need to link to.

I also meant to send you something, and the time crept up on me. Just like it does in the lab, now that I think of it. . .

2:44 PM  
Anonymous Selva said...

Fabulous! Very well done. A pleasure to read. The pictures are great!

3:18 PM  
Blogger The Mad Scientist said...

This compilation must have took forever to organize (with pictures too!) Hope you had some sleep last night. Look forward towards wasting lots of time reading all these entries.

3:52 PM  
Blogger Sunil said...

this seems like so much of work!! Excellent job....and a pleasure to read.

5:32 PM  
Anonymous Blog Carnival said...

Awesome! Just so you know, Tangled Bank is available in the Blog Carnival archive, along with lots of other carnivals (dare we say all?) - Enjoy!

5:43 AM  
Anonymous daen said...

Aaargh! Just when I thought I was going to get some work done, along comes a great big tasty mixed wodge of science-y stuff to munch on! :-)

7:56 AM  
Blogger Phila said...

What a cornucopia!

Wish I'd had time to do something (maybe next time)...hope I have time to check out all these fascinating links!

3:07 AM  
Anonymous feedster said...

aha
;-)

1:46 PM  
Anonymous Jim Online said...

This is a fascinating blog. I have reading a lot of blogs lately and I have observed that only a few ranks as informative. For starters, this will help people get a clear picture regarding the developments in Science. It is a known fact that a lot of people are unaware of such realities. Hence, a comprehensive rundown of developments is imperative.

6:46 PM  

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