Stories tagged History and Nature of Science

May
01
2009

A research group led by Dirk Brockmann at Northwestern University has created a computer model that predicts the spread of the 2009 H1N1 influenza virus in the US. (It uses a complex set of mathematical equations to describe the movement of people and virus.)

How can you track and predict the movement of something so small?: Follow the money, of course! (This is a colorized negative stained transmission electron micrograph (TEM) showing some of the ultrastructural morphology of the A/CA/4/09 swine flu virus. Got that? Good.
How can you track and predict the movement of something so small?: Follow the money, of course! (This is a colorized negative stained transmission electron micrograph (TEM) showing some of the ultrastructural morphology of the A/CA/4/09 swine flu virus. Got that? Good.Courtesy CDC/C.S. Goldsmith and A. Balish

(Brockmann was a guest on Minnesota Public Radio's Midmorning show today, and you can listen to it online.)

The good news is that, based on what we know now, and assuming that no one takes any preventive measures, we could expect to see some 1,700 cases of swine flu in the next four weeks. Because of the preventive measures being taken wherever a suspected case of H1N1 flu has popped up, we should actually see fewer cases. (You can see Brockmann's models here.) That's lousy if you're one of the folks who picks up the virus, but not a devastating number of cases. Of course, this is a rapidly developing, fluid situation, and things may change. Still, tools like Brockmann's model help to ensure that emergency supplies and other resources get to the places likely to need them most before they're needed.

Professor's Computer Simulations Show Worst-Case Swine Flu Scenario from Northwestern News on Vimeo.

Don't have faith in computer models? Well, a second research group at Indiana University is using another model, with different equations, and getting very similar results. That's a pretty good indication that the predictions are reliable.

You might remember Brockmann from a 2006 study that used data from WheresGeorge.com, a site that allows users to enter the serial numbers from their dollar bills in order to see where they go, to predict the probability of a given bill remaining within a 10km radius over time. That gave him a very good picture of human mobility, reflecting daily commuting traffic, intermediate traffic, and long-distance air travel, all of which help to model how a disease could spread.

Feb
16
2009

Evolutionary trees like the one Charles Darwin scribbled to illustrate his epiphany are still used today to help biologists understand and communicate the diversity of life. Like Darwin and his contemporaries, today’s evolutionary biologists are part of an ongoing effort to figure out how Earth's many species are related. As new tools help biologists to analyze evolutionary relationships, the tree of life changes and grows ever more complex.

How will biologists today and in the future to organize all of this information? No one knows for sure - but a number of computer scientists and software designers are taking a crack at it! In collaboration with biologists designers are creating programs that will allow researchers to share and search through enormous amounts of taxonomical information. Some programs, like UC Davis's paloverde, take cues from familiar web tools like WIkipedia and Google Earth, allowing users to search the tree of life from various perspectives and distances.

Beyond making research more accessible to scientists and the public, software tools like this will help scientists around the world work together in new ways - developing new medicines to treat constantly evolving diseases, new products and processes that take into account changing ecosystems, and to understand biodiversity on a local and global scale.

The potential of these tools is as big as the imagination of the designers and engineers behind them - what kind of tool would you create to help organize the tree of life?

Feb
12
2009

Charles Darwin: The great naturalist was born 200 hundred years ago.
Charles Darwin: The great naturalist was born 200 hundred years ago.Courtesy Public Domain
Today is the 200th anniversary of the birth of Charles Darwin, one of science’s most revered figures. Special events marking the occasion are planned throughout the world especially in England where he was born on this date (February 12th) in 1809. This year’s also the 150th anniversary of the publication of the famed naturalist’s most important work, On the Origin of Species by Means of Natural Selection, a book that revolutionized the science of biology, and one that - despite enormous amounts of evidence in its favor - remains controversial to this day. Born in the town of Shrewsbury, Charles Robert Darwin took after his grandfather Erasmus Darwin and from an early age showed a keen interest in the natural world, particularly geology, botany, and biology. While in college, a professor arranged for Charles to join the surveying expedition of the HMS Beagle to South America. It was during the five-year voyage that Darwin formulated his brilliant theory of evolution through natural selection. He returned to England in 1836 never to venture abroad again, and spent the next two decades writing out his ideas. On the Origin of Species was published on November 24, 1859, and sold out immediately. Five more editions were published during Darwin’s lifetime. He died April 19, 1882.

MORE ABOUT DARWIN
Darwin Online
Darwin Day site
Darwin Bicentennial at London’s Natural History Museum
About Darwin
Voyage of the Beagle (eBook)
Galapagos Islands in peril

Jan
06
2009

Year of Science Logo
Year of Science LogoCourtesy COPUS
The Coalition on the Public Understanding of Science (COPUS) kicked off Year of Science 2009 (YoS2009) -- a national, yearlong, grassroots celebration--this week in Boston at the annual meeting of the Society for Integrative and Comparative Biology. COPUS, which represents more than 500 organizations, is celebrating how science works, who scientists are, and why science matters.

YoS2009 participants—museums, federal agencies, K–12 schools, universities, scientific societies, and nonprofit and for-profit organizations from all 50 states and 13 countries—will host events in celebration of YoS2009. Regionally connected YoS2009 participants are bringing science to their local communities in innovative ways. To learn about YoS2009 events near you click here.

A special web site will help the general public learn more about this yearlong, national event. Highlights from the dynamic YoS2009 Web site include the integration of components from the newly launched Understanding Science web site, Flat Stanley explorations of science, the opportunity to name a new species of jellyfish or adopt a species for the Encyclopedia of Life, and a contest to build the most scientific pizza.

All of these events and activities foster innovative new partnerships that will bring science and the public closer together locally, regionally, and nationally—all in a growing celebration of science!

Dec
25
2008

Greetings from lunar orbit, Dec 24, 1968

Forty years ago the crew of Apollo 8 delivered a live, televised Christmas Eve broadcast after becoming the first humans to orbit another space body.

"The vast loneliness is awe-inspiring, and it makes you realize just what you have back there on Earth," Lovell said. Wired

First public radio broadcast, Dec. 24, 1906

Speaking of famous Christmas eve broadcasts, it's worth remembering that Reginald Fessenden made what is generally recognized as the first public voice-over-radio broadcast on Dec. 24, 1906.

Dec
21
2008

Catholic Pope salutes 400 year anniversary of Galileo and his telescope

Galileo telescope replica
Galileo telescope replicaCourtesy Michael Dunn
Pope Benedict XVI chose today's winter solstice to remark that the 400th anniversary of Galileo's use of a telescope is soon upon us. Galileo was condemned by the Catholic Church for supporting Nicholas Copernicus' discovery that the Earth revolved around the sun. In 1992, Pope John Paul II apologized, saying that the denunciation was a tragic error.

Benedict said understanding the laws of nature can stimulate understanding and appreciation of the Lord's works. Newsvine

International Year of Astronomy (IYA2009)

2009 has been designated International Year of Astronomy (IYA2009) by the International Astronomical Union (IAU) and the United Nations Educational, Scientific and Cultural Organization (UNESCO). I recommend checking out the International Year of Astronomy website for news and events.

The vision of IYA2009

The vision of IYA2009 is to help people rediscover their place in the Universe through the sky, and thereby engage a personal sense of wonder and discovery.

Learn more about IYA2009

Oct
29
2008

Iraqi National Museum
Iraqi National MuseumCourtesy US Department of State
The former director general of the Iraqi National Museum, Dr. Donny George Youkhanna, will give two presentations in the Twin Cities this November.

The first presentation, “Mesopotamia: The Beginning of Civilization,” will focus on the archaeology and cultural history of Iraq. It will take place on Wednesday, November 12 from 11:30 a.m.-12:30 p.m. in Sundin Music Hall, on Hamline University’s Saint Paul campus.

The second presentation, “Looting of the Iraq Museum: The Loss of a Nation’s Memory,” will focus on the status of the Iraqi museum, the restitution of antiquities from other countries, and the ongoing looting of Iraq’s archaeological sites. A panel discussion will follow. It will also take place on November 12. It will be held from 6:00-8:30 p.m. at the Weisman Art Museum on the University of Minnesota’s Minneapolis campus.

Both events are free and open to the public. More information about the events can be found here.

Oct
13
2008

A display on adult stem cells, here at the SMM: In fact, this exhibit features Catherine Verfaillie herself.    (Good looking out, BK)
A display on adult stem cells, here at the SMM: In fact, this exhibit features Catherine Verfaillie herself. (Good looking out, BK)Courtesy bryankennedy
Following the results of an evaluation by a panel of experts at the University of Minnesota, the magazine New Scientist published an article last week announcing that some of the data used in a groundbreaking study on adult stem cells had been falsified.

The study, performed at the University of Minnesota under the supervision of Catherine Verfaillie, is part of a line of research that seemed to indicate that adult stem cells, taken from bone marrow, are pluripotent—that is that they have the potential to develop into any type of cell. Previously, only embryonic stem cells were thought to be pluripotent, and Verfaillie’s research looked like it could eventually offer an alternative to the ethically complicated use of embryonic cells for research (which requires the destruction of an embryo).

Unfortunately, other scientists had trouble replicating Verfaillie’s results, which were published in the journal Nature. New Scientist began examining the research done by Verfaillie and her team, and found that key images in the research appeared several times in papers for different experiments, and, in the case of a related study in the publication Blood, were used twice in the same paper, but had been visually altered slightly, and flipped 180 degrees. New Scientist reported their findings to the University, which began a formal investigation of the matter.

The University just recently completed the investigation, and found that data in the blood article had indeed been falsified (the images in particular), by a former PhD student of Verfaillies’, Morayma Reyes. The University and Catherine Verfaillie have asked Blood to redact the study.

Verfaillie has stated that she was unaware of the problems with the published study, and while she didn’t believe that the data was deliberately falsified, she takes ultimate responsibility for the errors.

Reyes, who now works as an assistant professor at the University of Washington, denies that the images represent deliberately altered data, and blames the errors on inadequate supervision and training. She claims that she had neither the equipment (photo editing software) nor knowledge required to alter the images. The differences in the reoccurring images were likely the result of the inadvertent use of the image adjusting tools built into lab equipment, she says, and the duplication of a figure within the Blood paper was accidental. Reyes also feels that she has been treated unfairly by the University, and that the expert panel in the investigation demonstrated a clear “lack of expertise” in the field of stem cell biology.

Reyes’ full position can be read here. The University’s response can be found here.

The altered images, Reyes asserts, shouldn’t change the results of the paper, but the whole incident brings up some interesting issues on the process of vetting science. While the errors in the paper never should have made it past Verfaillie and the rest of her team, the process of peer review should have caught them anyway. Generally, before research is published in a scientific journal, the editors select several scientists in the particular field of the paper to evaluate and comment (often anonymously) on the paper. The review panel is meant to confirm that the methodology of the experiments and the interpretation of the results are sound. Research can then be recommended (or not) for publication.

Publishing research essentially formally submits it to the scientific community, and it’s common for other scientists to attempt to replicate experiments, especially if a study makes particularly striking claims (like adult stem cells being pluripotent). The work of other scientists in replicating results is, obviously, essential to the scientific method—in this case is was what finally drew attention to some of the irregularities in Verfaillie’s team’s work.

Reproducibility can be a tricky thing, though—difficulty in repeating results doesn’t necessarily mean that they aren’t reproducible. (Here’s a good article on repeating and reproducing results.) But the problems in reproducing these results drew attention to the questionable data, which brought up another aspect of scientific vetting: the University’s investigation into academic misconduct. If the problems with reproducibility seem to come from data being changed, added, or omitted to strengthen a conclusion, then there could be a serious problem. This sort of misconduct undermines scientific progress, and can call into question the reputation of the institution it came out of and the validity of other research performed there. And if Morayma Reyes seems a little extra defensive in her letter, it’s understandable, because being accused of academic misconduct is a big deal, and no good for your career and future work.

The subject of the research further complicates the situation—this isn’t the first time issues of academic dishonesty have come up with regards to stem cell research. In 2006, a Korean scientist’s claims that he had cloned human embryos (thereby eliminating the need to destroy new embryos for stem cells) turned out to be based on lies. There’s a fear that the potentially huge medical payoff of stem cell research, as well as the ethical debate surrounding the use of human embryonic stem cells, could lead to science that is less than completely thorough, or even situations like the Korean controversy. And that’s bad for science in general. There’s also the thought that errors that are unintentional (as may be the case with Reyes’ images) could be the result of “pathological science,” where results are steered in a particular direction by scientists because of “subjective effects, wishful thinking, or threshold interactions.” It doesn’t have the same ethical problems, but pathological results aren’t a whole lot better for science than straight-out misconduct, and it’s a serious potential pitfall with the benefits of stem cell research waiting out there as temptations.

So there you go. It looks like things are, for the most part, being handled appropriately in this situation, but it’s an interesting window into scientific process.

Any thoughts? Does it seem like the vetting process of science is lacking in some way? Or is it maybe too thorough? Professor Reyes, I imagine, would argue that too much has been made of this situation, and there are many who argue that the process of peer review limits the communication and dissemination of scientific ideas.

Or, even better, does it seem like I got something wrong here?

Let’s have it, Buzzketeers.

Sep
24
2008

Charles Darwin, photographed by Julia Margaret Cameron, 1868
Charles Darwin, photographed by Julia Margaret Cameron, 1868Courtesy Julia Margaret Cameron
I believe I have mentioned this film before - but have you ever seen the documentary "Flock of Dodo's"? It is a well made (imho) film that creatively and sometimes humorously, discusses the evolution vs. intelligent design debate. The thing that I find most interesting about this film is that it shows something that I think is important. While I may think people who support intelligent design or creationism are wrong, many scientists who argue with them act like uppity jerks. Its not likely a debate one side is going to "win" but we can all at least accept that and be civil.

Now, if you want to be ready to argue for evolution, Scientific American has put together a nice little web feature that covers the topics of creationism in the classroom, a state by state breakdown of the creationism in schools controversy, 15 answers to creationist nonsense (again, could be a bit less harsh in the language here) and a discussion about how scientists ought to approach religion and its followers.

Sep
19
2008

CSI: The Experience will open here at SMM on October 15.

One aspect of crime scene investigation is forensic entomology: the use of insects found on or near a body to help determine the time, manner, and location of death.

And we're fortunate that Valerie Cervenka, the first female board certified forensic entomologist, lives here in St. Paul. She's our Scientist on the Spot right now, so you can read about her work and get her answers to your questions.

And, Buzzketeers, do we have something "special" for you... Lots of forensic entomology studies are done using pigs, because (according to Jessica Snyder Sach's Corpse:

"The soft, near-hairless skin of a domestic pig closely duplicates that of a human, and that the torso of a luau-size porker parallels that of a 160-pound man."

Pig, @2pm, 9-18-08: Our pig, fresh from the freezer.
Pig, @2pm, 9-18-08: Our pig, fresh from the freezer.Courtesy Liza Pryor

That is, the skin, muscle/fat ratio, and other characteristics of pigs are reasonably good approximations of humans'. In death, what happens to a pig, and when, is pretty similar to what happens to human corpses. (If you think that's unpalatable, consider that the other way we can calibrate insect evidence is to do controlled studies at places like Tennessee's "Body Farm," where researchers observe what happens to people instead of pigs. You can search Buzz for the term "body farm" if you're interested in that: we've done a few stories.)

So we've obtained a young pig. (Don't worry: the pig died of natural causes.) And we've put it in a cage, with a webcam, and we're letting it decompose. The camera records a still image every 15 seconds, and we'll eventually turn all those photos into a time lapse, which Val Cervenka will help us interpret. Pretty cool. Pretty gross. And all in the interest of science.

Why didn't we wait for the exhibit? Well, insect activity slows dramatically or even drops off to nothing once the outside temperature gets to about 50 degrees. To follow the pig through most of its stages of decomposition, we had to get it going now.

Want to see what's going on with the decomposing pig right now? Click here. But don't say we didn't warn you. It's graphic.