Next Generation Microscopy: Goodbye Purple Fingers - No Stain Microscopy

Twenty years ago when I took Microbiology I learned about staining. Tissues had to be stained in order to 'see' the cells and cell organelles. Under a light microscope it all looks clear or pinkish and transparent. Add a couple of drops (or micro drops) of a certain dark stain would attach to the walls of the cell or organelle and then * wa-la* Contrast.

And for some reason all of the important stains were blue, hence the reference to blue fingers because you get some on your hands, lab coat, apron, table, etc.

Example stains include Methylene Blue Stain, Methyl Blue Stain,Indigo Stain....

and my time favorite, because it was the first staining technique I learned, was Crystal Violet or Methyl Violet used to differentiate Gram Negative Bacteria from Gram Positive Bacteria.

Microbiology lab was the first lab I took that made me feel so empowered. Lab was twice a week and I never minded staying for the whole time. It was hands-on learning and application of stuff I was learning in the class. I was holding a vial of something putrid and I was going to figure out what it was with stain and petri dishes. I felt like MacGyver. Do my pre-med, biology, chemistry, and biochem majors feel me? Aaah memories. My blue fingers were a badge of honor (and I didn't bite my nails much that semester.) But alas, those days may be no more. Some super-duper microbiology genius has helped us see the invisible without stain. Read more about it below.

Repost of NSF Press Release 08-218

Microscopes have revolutionized the practice of science, especially in the fields of biology and medicine. Just a few hundred years ago, gaining the ability to study what was previously unobservable opened up an entirely new world. Today, imaging techniques remain indispensable to clinicians and researchers who regularly diagnose medical conditions and work to develop new treatments.

Test results can often take hours or even days because cells or tissues must be subjected to lengthy fixation and labeling processes, sometimes called staining, in order to visualize and distinguish cellular components. In addition to long processing times, staining procedures often include harsh treatments or conditions that alter the tissues themselves, making interpretation of results difficult.

A newly developed label-free imaging technique called stimulated Raman scattering (SRS) will likely revolutionize biomedical imaging in research and diagnostic laboratories. A team lead by Sunney Xie at Harvard University reported this new technique in the December 19 issue of Science.

"It is a big step forward in terms of biology," said Xie. "SRS is a powerful imaging modality with widespread applications on many fronts of biology and medicine. This work compliments an earlier technique we developed with funding from the National Science Foundation, adding a new imaging modality to the vibrational microscopy field."

The key to this new chemical imaging technique is the use of two lasers with different frequencies. Researchers visualize samples by tuning the laser frequencies to match the vibrational frequency of a specific chemical bond. Each type of molecule within a sample, including nutrients or drugs, is detectable at a unique frequency. By combining sample data collected at numerous frequencies, researchers can produce a high-resolution 3D image of the sample. SRS microscopy represents a big gain in biomedical imaging because it avoids labor-intensive sample preparation and autofluorescence, or "background noise", associated with traditional fluorescence microscopy.
Xie is enthusiastic about the ways in which SRS imaging will facilitate progress in many fields. "Applications of SRS imaging range from mapping distribution of small metabolite and drug molecules in cells and tissues to medical diagnosis of cancer. Neuroimaging is another exciting area of application."

Media Contacts

Lisa Van Pay, NSF (703) 292-8796 lvanpay (at) nsf.gov

Lily Whiteman, NSF (703) 292-8070 lwhitema (at) nsf.gov

Principal Investigator

X. Sunney Xie, Harvard University (617) 496-9925 xie(at)chemistry.harvard.edu

Science Nobel Prize Winners Announced

I know the US Political Theatre has most of us wide mouth. But the world of science and discovery is steady at the helm. The Nobel Foundation has named its 2008 winners in the science categories.

Doctors Osamu Shimomura, Martin Chalfie, and Roger Tsien share The Nobel Prize in Chemistry for their discoveries of the green florescent protein in jellyfish
Here’s what they did.

Doctors Yoichiro Nambu, Makoto Kobayashi, and Toshihide Masukawa share The Nobel Prize for Physics for their discoveries of broken symmetry dynamics. Don’t even ask me what this means. I understand the chemistry and physiology/medicine award. I need to go back to school to figure this out. But nonetheless it’s important. Bone up, read about it here.

Doctors Francoise Barre-Sinoussi, Luc Montagnier and Harald zur Hausen share The Nobel Prize in Physiology or Medicine – the discoverers of the Human Papilloma virus and the HIV Virus . By the way this award is for most any life science discipline. Dr. Robert Gallo also did some key research on the HIV virus wasn’t co-award the prize. Science Drama.

Go to Happy Hours this weekend and impress the socks off of everyone. For good measure throw in some chatter about the folks throughout history who were worthy but did not get the award. The most notable un-awardee is perhaps Rosalind Franklin who did all of the real work that Watson &Crick are now famous for. Coincidentally her research work cost her her life.

Promoting Diversity in STEM: Society of Wetland Sciences offers Conference Travel Award

The Society of Wetland Scientists (SWS) announces the availability of undergraduate student awards for travel to attend the annual SWS meeting –June 22-26, 2009 in Madison, Wisconsin.

The SWS is committed to increasing diversity in its membership and is offering full travel awards and mentoring at the meeting for undergraduate students from under-represented groups (African-American, Latino-American, Native American, Pacific Islanders, and persons with disabilities).

SWS Diversity Program: 2009 Undergraduate Mentoring Awards

These awards are supported by the National Science Foundation and several SWS Chapters(Mid-Atlantic, South Atlantic, North Central, Western, and PacificNorthwest). ***All Travel Expenses paid (air, hotel, meals, and conference fees***. The areas of interest of the student participants range from freshwater to marine and involve a wide variety of organism types.

Undergraduate participants must be citizens or permanent residents of theUnited States or its possessions. An undergraduate student is a student whois enrolled in a degree program (part-time or full-time) leading to a baccalaureate or associates degree. Students who are transferring from one institution to another and are enrolled at neither institution during the intervening summer may participate. Spring 2009 graduates are eligible as well.

Application materials and additional information are available from:

Dr. Frank P. Day

Old Dominion University

fday[at]ODU.EDU

pdf of application

Application deadline is November 28, 2008.

There are additional Travel awards for student members of SWS offered on a chapter by chapter basis. Visit SWS STUDENT TRAVEL AWARDS to look up information about eligibility in your region.

Presidential Candidates Stand on Science

The other day, I blogged about the Presidential Candidates’ stands on science. STEM is the foundation of this nation’s prowess, security, and success. Therefore sound science policies and developing other policies with sound science and advice is terribly important.

Too bad there won't be a 4th Presidential Debate that's all about Science and Education. But we've got the next best thing - ScienceDebate2008. It is an online forum where the candidates provided answers to 14 key Science questions. The goal is to raise public awareness of science, technology, and innovation and call attention to informed decision-making at higher political levels. You can read their answers and offer comments and offer new questions.

I am biased (I support Obama), but my first response to the candidates side-by-side answers is that the two definitely see science differently.

Obama details his interests and comprehension of the importance of the STEM pipeline. He proposes funding science & math education from K-12 through graduate education and early career research grants. He focuses on supporting science through agencies like the National Science Foundation.

McCain doesn’t even mention a single science agency and all of his focus is on technology and entrepreneurship. Basic research happens at colleges adn universities and through scientific agencies like NSF, NASA, and NIMH. Business innovation of technology and discovery takes place AFTER graduate students and post-docs work out all of the kinks. I am disturbed by McCain’s limited comprehension STEM and its work culture. He completely disregards the role of academics in science research, and it makes him seem so out of touch. He complete focuses on tech-related industries (I guess because of the potential for entrepreneurship) and ignore the basic sciences such as life sciences and physical sciences. And I’m still sore about the comment about science research being a wasteful pork earmark.

Let me share something with you all. The ability to get federal research money for science is based on a very strict, very competitive peer-reviewed system. You have to write a detailed grant explaining why you want the money and the impact the research/results will have on the world. Science is about knowledge – gaining knowledge, clarifying information, and disseminating knowledge. Even great ideas that might possibly change the world get denied because of lack of impact. Getting research money is no easy task. Even for my graduate-level research monies I had to jump through several hoops. No one passes this money out. There is no special money set aside for pet science projects –of any kind. Everyone must compete and demonstrate professional ability before any money is granted.

Update: From Campaign News from AAAS Policy Alert Newsletter.
On Sept. 26 the Obama campaign released a revised plan for science, technology, and innovation and a letter signed by 61 Nobel Prize-winning scientists who have endorsed Obama. On Sept. 29 Senator McCain released a radio ad reinforcing his past record on stem cell research and calling an Obama ad claiming that he has "stood in the way" of stem cell research "misleading." And in a speech last week at the Clinton Global Initiative, McCain reiterated his commitment to addressing global warming.

Stay informed!
I can’t wait for the VP Debate tomorrow.

Going Public with the Scientific Process

The Scientific Process is the heart and soul of all science. The Scientific Method you learned in school is part of it, but not all of it. Science, like all human endeavors, is subject to human error, interpretation, value and judgement. Science is the process of creating, supplementing, and updating the world body of knowledge. The March 14, 2008 issue of Science magazine has a letter about the Scientific Process. I am posting the entire letter below. All emphases are mine.

******************

The idea of using framing strategies to communicate science to the public has recently been taken up in scientific forums (1, 2), the mainstream media (3), and the blogosphere (4, 5). Most participants in the framing science debate limit their notion of scientific information to scientific facts. However, confining science messages to just the facts interferes with public understanding of science as a systematic, logical process of human inquiry and effaces the distinction between data and scientists' reasoning about data. To communicate successfully, we should focus on scientific process by emphasizing two important elements of scientific rationality: skepticism and dynamicism (6, 7).
Scientists deliberately integrate skepticism into their procedures by trying to refute their own hypotheses, retaining them only when confronted with compelling evidence sought through carefully controlled procedures. Scientists tend to shy away from revealing the intrinsic skepticism of science to the public, fearful that it will open the door to doubt about the validity of their conclusions. But communicating only the facts of science (framed or unframed) destabilizes public confidence in science. A fact doesn't allow science communicators to reveal, justify, and ultimately promote the skeptical reasoning process that helps make scientists more confident that their reasoning is correct.
Science is also dynamic; it is a cumulative enterprise that requires scientists to situate their instrumental activities and interpretations against the evidence that has come before and to alter them in light of new evidence. Insisting that new data be interpreted within the context of past and future data will ferret out and correct error over time, but it means that a fact cannot, by definition, be anything more than the (ephemeral and fallible) consensus of scientists at a given point in time. A "just the facts" strategy can and often does backfire, ultimately fueling public alienation from science. When scientists inform the public of "facts" (like the "fact" widely disseminated in the 1970s that all dietary fats are bad for us), and then that "fact" is refined or altered (now we're told olive oil is good for us), the public is justifiably confused. Studies suggest that the public tends to regard normal scientific refinement and self-correction as equivocation or incompetence (8-10). Instead of sweeping uncertainty under the rug, science communicators should help the public understand the logical and systematic procedures by which scientists confront it.
The true majesty and promise of science lies in its systematic, logical, skeptical, and dynamic reasoning procedures. "Successful" science communication should not be regarded as any message that enlists public support for science. Rather, we should define "success" in scientific communication as achieving a public that celebrates scientific reasoning procedures.

Ruth Cronje
Scientific and Technical Writing Program
University of Wisconsin-Eau Claire
Eau Claire, WI 54701, USA
References
M. C. Nisbet, C. Mooney, Science 316, 56 (2007).
M. C. Nisbet, D. Scheufele, The Scientist 38, 38 (2007).
M. C. Nisbet, C. Mooney, "Thanks for the facts. Now sell them." The Washington Post, 15 April 2007; Outlook section, p. B03.
AAAS News Blog, "Science has a 'serious marketing problem,' says Google founder Larry Page," 17 February 2007; available online at {www.aaas.org/news/releases/2007_ann_mtg/127.shtml}.
P. Z. Myers, "What if the right role for science is to shatter the frame?" Pharyngula, 7 April 2007; http://scienceblogs.com/pharyngula/2007/04/what_if_the_right_role_for_sci.php.
J. Habermas, The Theory of Communicative Action, Vol. 1: Reason and the Rationalization of Society, T. McCarthy, transl. (Beacon Press, Boston, 1984).
H. I. Brown, Rationality (Routledge, New York, 1988).
B. Wynne, Environment 31, 10 (1989).
B. B. Johnson, P. Slovic, Risk Anal. 15, 485 (1995).
B. B. Johnson, Risk Anal. 28, 781 (2003).

Government Funded Research on African-American Children - Math & Science Scores improve

The Good News: The Achievement Gap in Math and Science is closing between both African-American and Hispanic students and white students in elementary school math, and between African-American and white students in elementary and middle-school science.

This is Government funded/sponsored research and it is your tax money at work (US citizens). In light of the dialogue concerning the sewer study in black neighborhoods, I realize there is a huge misunderstanding about government funding research. I hope to set the record straight. Most of our nation's (and most other nations, too) science, technological, and engineering innovations are funded with public money. The National Science Foundation, the Department of Energy, the National Institutes of Health, the National Institute of Mental Health, Centers for Disease Control, and even the Smithsonian Institute are all major funders of STEM research. Private foundations also leverage funds to researchers.

Though each organization has its own forms to fill out and hoops to jump through, all pretty much have the same process.

1. Organizations ANNOUNCE the availability of funds for research. The Agency announces funds are available and each major program (discipline related) get so much of the pie. Not every program gets the same amount of money (that's a completely different topic to tackle). Let's take the field of Engineering for example - program divisions would be Materials Engineering, Electrical Engineering, Air and Transportation Engineering, and so on.

2. Researchers (most often from colleges or universities) survey their portfolio of research and see if they are doing something that might fit the bill. Researchers are often college professors (faculty) who have earned doctorate degrees in their field of study. Researchers train graduate students (those pursuing master's and doctorate degrees), so they can apply for and use this money, too. Sometimes, there are special funds set aside ONLY for students, faculty cannot apply.

3. Researchers write a proposal for the money (a grant) that outlines what type of research they are doing (or will do) and how they will use that money. Grant writing is a long and grueling process - sometimes. Essentially, you are writing a research proposal to be evaluated by the most critical and qualified people in your field. There is way too much money on the line to just give it to someone who has a neat idea, but doesn't have the ability, capability or proven track record to get things done.

4. In exchange for the money the researchers must adhere to all legal boundaries (state, federal, and professional) as well as ethical boundaries. These are also considered in the grant proposal. Any red flags and a researcher has to re-do the whole proposal or sometimes is disqualified from funding for that round. Researchers are also expected to disseminate results - not only to other professionals in his/her field, but to the public as well. Why? Because the public paid for it. Also, this new information is knowledge designed to enhance/enrich our lives. Others (practitioners, students, and other researchers) can use this information to make decisions about policy, their lives, business, pursue future research, etc.

The story above is such as example. And can't you just imagine the many applications of this finding and the study itself informing struggling school districts? So, to clarify, government sponsored funding is typically how most research is funded AND it isn't designed to take advantage of any group of citizen. It is a very critical process and though the jargon can be overwhelming to non-scientist/engineering, it is open and subject ot public scrutiny.

Stay informed.

The Science of the Sewer Study in Poor Black Neighborhoods

In response to the dialogue about this case, I have added some links that are a follow-up. Specifically, I want to address the science or scientific processes involved in this type of research. Here is the SOIL COMPOST STUDY TO REDUCE LEAD HAZARD FACT SHEET.

Here is the abstract or summary of the research experiment. The study was published in the peer-reviewed journal Science of the Total Environment. The journal is an international medium for publication of original research on the environment with emphasis on changes caused by human activities. It is concerned with changes in the natural levels and distribution of chemical elements and their compounds that may affect the well-being of the living world, or represent a threat to human health. Papers in applied environmental chemistry and environmental health sciences are particularly encouraged. This study falls well within the purview of this publication.

I do understand the environmental justice concerns of this research specifically with this research group, as noted by Francis Holland. I'm not dismissing his or others concerns. However, I think it is important that those who are most vocal about this issue demonstrate a basic comprehension of how this type of research is conducted and what this study found.

Let me break a few more things down.
In addition to Institutional Review Boards (see note in previous post), the peer-review process is another stop-gap for making sure appropriate procedures and ethical measures are followed in research. Research that is believed to be problematic is investigated and not permitted to be published. There are also number of professional reprimands for researchers are proven to be unethical or inappropriate when researching or reporting results.

The Abstract - rewritten
High lead concentrations in urban industrial areas are a big problem and can cause many health problems in people, but there is no one program to get rid of lead in soils, unless it is a big nasty spill from a company or factory. So there are many people who are exposed to lead in soil, but there is no feasible and affordable solution at hand. The researchers selected lawns in contaminated neighborhoods where the ground contained a fairly high concentration of lead which can get into the human and animal body systems. They used a commercially comparable compost, organic material from animals, that contained a fairly high concentration of iron and phosphate, and spread it over the lawns. Iron and phosphate can grab the lead in the soil and keep it from getting into the body system of people and animals. Iron and phosphate are also great fertilizers to improve the health and appearance of lawns.

The lawns were tilled, or dug up, and the compost was applied. They sampled the soil in the lawn several times to compare the levels of lead in the soil in various locations in the yard (near to the home vs farther away from the home) and many times over the course of the year. They compared the level of lead before the compost was applied and many times after the application.
At the end of the experiment, the lead concentration that can get into the body was much lower. The lower concentration of lead was more notable at areas closer to the home, where the risk of picking up lead was higher. At the more distant parts of the lawn, the treatment didn't lower the lead concentrations much, but there was always a lower concentration of risky lead in those parts of the yard. Plus, the lawns were healthier and more attractive at the end of the study. This research met its objective of finding a possible and feasible way of reducing lead in soil without having to dig up the whole yard and discard of the contaminated dirt in some undetermined place. This research is particularly important because it may provide an affordable solution to reducing lead poisoning risk in children.

Sewer Study in Poor Black Neighborhoods - Good Science or Bad Policy?

Recently, some media outlets have cried a possible foul against the scientific research community concerning a study that fertilized lawns with human and industrial waste as possible remediation to lead poisoning. NPR News & Notes featured a piece about Scientists Under Fire for Sewage Sludge Study. Francis Holland ranted about it too on American Journal of Color Arousal. Study participants were all Black and lived in poor urban neighborhoods. Since this research is 'government funded' some are asking whether these participants were intentionally targeted and if the government is 'deliberately experimenting on vulnerable citizens'.

I realize that the black community is still untrusting of scientists and science research. And this issue has several groups like the NAACP up in arms claiming Tuskegee type issues. What is the main problem? That the recent research was done in those neighborhoods or that the research was done and people were harmed? If people were harmed AND they were not fully alerted to the dangers (I doubt that) AND they were not treated AND the incident was swept under the rug, then there is a point and the anger is justified. But according to the press stories none of these scenarios seem to be the case.

It seems the matter of research can’t be addressed objectively among the Black community because of the sensitivity regarding the Tuskegee Experiment. The Tuskegee Experiment was a sad page in history, but let's keep things in perspective. 1. Monitoring the unchecked effects of syphilis in blacks was a meaningful experiment - at that time. Back then, Syphilis was unchecked in everybody and because of racist beliefs, many people really believed that similar treatment in blacks as whites would have been a waste. As sad it is sounds, the doctors wanted to prove (not just provide anecdotal evidence) that Syphilis harms black people just as bad as Europeans. 2. What made the Tuskegee Experiment egregious was the fact that a cure had been found and they did NOT Inform the participants.

Since that case, the laws and ethics of clinical research have improved dramatically. Remember the finding that hormone therapy might be harmful to menopausal women? They pulled that treatment and halted that study. That's how research works now. Also, Institutional Review Boards (IRB) are VERY stringent and serious about critiquing ALL research before ANY experiment is done. They make sure everything is proper and safe and legal. They follow strict federal and state and professional research organizations’ procedures and ethics guidelines when conducting ANY research with living subjects, especially human. They err on the side of safety and caution. These Boards are not comprised of a group of like mined scientists who co-sign each other’s research. These boards consists of scientists, a doctor or veterinarian, lay persons from the larger community (such as clergy or politicians or teachers or community activist). And you best be sure the university administrators have lawyers look over things for liability as well.This case is a perfect example of a sensationalized story that was presented to speak to people’s fears and ignorance about science or research processes. I understand the sensitivity we have that poor, marginalized people may be being taken advantaged of in research studies. But that fear and the campaign against research is harmful.

This is a matter alerts me of the crucial need to increase the public’s awareness of science and research. The need to increase scientific literacy among people is not just limited to the marginalized and under-educated, specifically black people. I keep discovering that even presumably well-educated black people are still prone to get keyed up emotionally and are largely ignorant about science and how it proceeds.

Which leads me to address one more issue - Government funded research does NOT mean government directed research. Scientists develop hypotheses from direct observations. Hypotheses aren't handed down to scientists. This research was undertaken by a team of academic researchers. This was an idea that they developed, perhaps born of real-life issues they were encountering - lead poisoning of nearby residents (who happen to be poor and black). The researchers secured funding to undertake this research - they asked for the money, the government was not trolling around for researchers willing to make guinea pigs out of people.

Human Origins in Africa - Weekly Science update

Palentologists and Population Geneticists have discovered and confirmed that our human ancestors originated on the dark continent. "A team of Genographic researchers and their collaborators have published the most extensive survey to date of African mitochondrial DNA (mtDNA). " The genetic material of the mitochondria, or powerhouse of the cell, is high conserved and has a very low mutation rate compared to nuclear or regular DNA. When sperm and egg unite, they each bring their fair share of nuclear DNA - 23 chromosomes. 22 Somatic or body chromosomes and 1 set of sex chromosomes to determine the gender of the baby. The chromosomes are the packages of ALL of your genes. Both the egg and sperm are single cells, but the egg, which is a bit larger than the sperm, also houses other cell organelles, including the mighty, mighty, mitochondria. So if you did a cheek swab, a la Maury Povich style, your mitochondrial DNA is exactly your mom's so on down the line.

"Mitochondrial DNA, inherited down the maternal line, was used to discover the age of the famous 'mitochondrial Eve' in 1987. This work has since been extended to show unequivocally that the most recent common female ancestor of everyone alive today was an African woman who lived in the past 200,000 years. Paleontology provides corroborating evidence that our species originated on this continent approximately 200,000 years ago."

So this backward game of chasing down the mtDNA has to deadline somewhere - that's to mitochondrial Eve. But the researchers found that there are 2 dead ends. Both deadline on the African continent, but separated geographically - eastern and southern Africa - and over many tens of thousands of years.

Check out the full article on ScienceBlog: Humanity nearly split in two, study finds

Pre-College Computer Science Camp for youth

Attention to all the College Park, Maryland Area!!

The Dept of Computer Science at the University of Maryland is sponsoring their annual Passport Program this Summer for middle and high school students interested in computer science or computer programming. This program is offered at no cost to the student.
Free Supplemental Education in Computer Programming. This beyond just application or using a computer. These classes are about creating and designing software. Wow! What a fantastic opportunty for students. It looks good on college applications. Makes your child or students more employeable or college ready!
The online application needs to be completed by the May 30, 2008 deadline. Since, I so obviously overlook Technological sciences so often, I'm trying to make amends here and there. Please share this information with any student, parent or teacher that you think might be interested.

Evolution Debate - Science vs. Faith

The Debate about teaching Evolution in Science Classes and whether to include lessons about "alternative" theories has been a matter of science education contention forever, it seems. Feb 29, 2008 issue of Science magazine reported that Florida Standards Support Evolution--With a Twist.

One of the main counters to teaching evolution is a semantics issue. The word theory ties counters' panties in a knot. In lay terms, a theory is a guess, a whim. But in science, it is a firmly supported statement (hypothesis) that has withstood strong contests. A theory is a big deal, it pretty much set and that's it. For example, gravity is a theoretical concept (of physics), the Law of energy conservation is 'just a theory'. So when anti-evolution legislators in Florida wanted to undermine science education standards and dupe the public into thinking evolution was just sample fancy theory and tried to legally change the text books to say "evolution is a theory", suave scientists and science educators complied...Fully. They changed the language through out to make it parallel. They applied the phrase to every major, time-tested scientific concept. So not only is evolution explained to be a "scientific theory of evolution" but also things like "the scientific theory of photosynthesis".

Gotcha!!

But this matter is serious. Religious zealots are serious about undermining quality science education. Why? Many reasons, one of the best answers comes from a Florida legislator who tried to re-word the science standards for evolution, Donna Callaway. She says "People have asked me why I don't question math concepts or grammar," she explained to Science. "I tell them, 'Those things have nothing to do with life. Evolution is personal, and it affects our beliefs.' "

My response to that statement....WOW. That is naive. Plus, that's apple-picking. Even Nisbet commented on this issue in his blog posting Why the PZ Myers Affair is Really, Really Bad for Science. I completely share the sentiments of this blog. In fact I was having a great discussion with a friend about evolution distorting people's spiritual beliefs. I think it is crap to assume studying science makes one more likely to become atheist. I just don't buy that evolution affects our beliefs -- assuming one understands the concept. That's the problem. Too many people are guessing what they think it means. And what makes it right for some people to tell us what is right to impact out beliefs. I guess studying science is heresy -- leads to critical thinking, discernment, challenges to authority. Damn independent thinkers. Can't have that. Let's protect them from themselves...Change the science standards.

But for many people (outside of science) it seems a plausible correlation. Many of my peers are atheist, agnostic, or spiritually neutral. But none that I know are that way because of studying science. They were that way long before studying science. And I also know scientists of faith, who were also that way before studying science. Go figure.

Is there a relationship between science and atheism? Perhaps. But you can't automatically conclude it is causal.

Darwin Days are here again

February 12 is Charles Darwin's Birthday. Though impossible, if he were alive he would be 199 years old.

Darwin's contribution to science and biology have had a tremendous impact. Darwin's Theory of Natural Selection has shaped biology research and the study of evolution. Check out the links to learn more about evolution and natural selection -- the bedrocks of life science.

National Science Foundation - 2007, A Year in Review

As a receipient of a fair share of NSF money, and as a show of appreciation of your financial contributions to my education and research, (yes, thank you U.S. tax payer) here is a look back at some of the NSF-supported advances and activities reported last year.

NSF Discoveries - 2007
You can check on this one daily and get a new morsel of great information everyday.
I missed the one about children's behavior and academic acheivement and career success. I'll definitely be pulling some of these out and serving up as main dishes at a later time.

Enjoy your serving of science.

Ohmigosh!

I've been reviewing my entries and I am SHOCKED. The number of typos is insane. Please forget that I have advanced college degrees. And forgive me as well. I'll try to clean them up here and there as I go.

But this does bring up a great point about the scientific process - YOU ARE NEVER DONE. There is always a critique or two. There is always room for improvement and revision. And most any scientist can attest to that - you are always revising and updating a hypothesis, a question, an experiment, an interpretation...something.

party on

Helping people overcome their aversion to science

Resistance to science has important social implications, because a scientifically ignorant public is unprepared to evaluate polices about global warming, genetically modified organisms, stem cell research, and cloning.
An excerpt from Childhood origins of adult resistance to science in Science Magazine 18 May 2007 issue.

Many Americans are resistant to learn about new technologies, evolution and natural selection, or complicated health care issues. Why? Because people have a hard-time accepting information that conflicts with their personal construct and understanding of the world.

Resistance to science, technology, and math (STM) education begins early and stays throughout life for most people. Usually because of a dissatisfying experience with STM during the formative years – middle and high school grades, many people shy away or outright reject information about our advancing knowledge in these areas.

Students and citizens are not empty vessels. No, they have a pretty broad idea of how the world works. These ideas may not be accurate but these ideas are ‘true enough’. And for many people they learn about new things from their personal expert -- someone in their social circle, someone they trust to be right or believe to be most knowledgeable.

Now, consider this: If a person is resistant to science since childhood, he/she doesn’t know any scientists, and she/her has no real idea of how science works, then how should they react to all of this new information? Why should they believe want the scientific community says about a matter? Why should they chuck out what they believe and know to be true?

One of my science education professors warns that we should not “expect students to replace one fairy-tale for another”. The students’ ideas and comprehension of the world are established, even if it is inaccurate. Just because you tell them what is correct and they provide the correct answers on the tests, doesn’t mean they will accept it as true. Especially for controversial lessons about evolution, students will take the test and then declare they believe none of the information provided by the instructor. Why? They failed to update their world-view.

So, how do we teach people about the world so that they can update their brain computers? We let them discover the phenomenon. Active learning through manipulation and experimentation is essential if people are to REALLY learn more about the world and about science. Teaching science as a laundry list of facts doesn’t help people become more scientifically literate or able to evaluate policies. However, meaningful learning experiences do give students and citizens the opportunities to figure things out for themselves.

Unlike the personal expert who can be vouched for, the scientific community has no such social capital with the general public. That’s not how science works – usually. The results speak for themselves; the proof is in the pudding. Our voucher system is the experiment or rather the experience. Science is best learned by doing it. Let people try things out, test assumptions, research perceptions. When people can figure things out for themselves that’s when people will resist science less.

Teaching science via active pedagogy

Far too many students enter and leave science classes memorizing the products of scientific endeavors without knowing what science is. They fail to understand that science involves the observation of natural phenomena, formulating hypotheses, and testing hypotheses. Having served as a resource scientist at an urban high school, I realized that these kids, no matter how bright and promising, were not at all cut out for college science courses. While delivering content knowledge in life science to students, I realized that it was just as important to help them discern what science is. As a scientist and an educator, my objective is to engage students to become active learners -- to ask questions, design experiments and test hypotheses. Specifically, I think it is important for students (high school, college and adult learners) ro have authentic science experiences. Such activities (also called problem-based or inquiry based lessons) can help foster lessons related to scientific processes.

STATS suck!

I've been pouring over data all weekend. I keep finding missing data (very good, valid data) that I somehow overlooked. Then I forget what I should be doing. Then I get weary of doing anything.

For me, confirming data points, checking the descriptive and frequency statistics is the not-so-sexy part of science. I know other people who LOVE it. (crazy scientists). My data set is so large. I intuitively know what I want to do, what columns & rows I want to summarize/compare. but I can't figure out this dang stats package language sometimes. What hoops do you want me to jump through SPSS 15.0? Would Xcel better? or Access. ah shucks, do them all.

More Science Drama

Seems there's plenty of scientific misconduct to go around. And it looks like Asia has been very, very, naughty (or at least a few of her nationals have been representing thier mother continent poorly.)

Here are some quick links to a number of recent articles publshed in Science Magazine.
Japan's Universities Take Action
Former Hwang Colleague Faked Monkey Data, U.S. Says
Online Sleuths Challenge Cell Paper
How Young Korean Researchers Helped Unearth a Scandal …

Interestingly, there may be a reason why it is happening. The pressure to perform. This doesn't justify the dishonesty. But it does help us understand why. Read SEED magazine's article about such issues: Scientists Behaving Badly

And there may be insight into why such cases of academic dishonesty and scientific misconduct can go undetected -- the process of peer-review as it currently exists. Fellow scientists check to see if the submitted research is interested and important, not necessarily factual. Fellow scientists can't possibly know if the data has been mismanaged, altered or made up. If it sounds plausible, then all is fine. Learn more here: And How the Problems Eluded Peer Reviewers and Editors
Usually, the first line of defense to dishonesty is within the researcher's own lab. If the lead researcher is repressive then this can limit honest discourse about the project and discourage subordinates from speaking up to others. After all, the lead researcher may hold the strings to the younger researcher's career or visa (if she/he is a foreign national).

Science Drama: Another lesson in Scientific Processes

A group of molecular plant biologists recently retracted their research article that was published in Science Magazine 2005 (volume 309, p. 1694). Read original retraction here. There were several gross anomalies with the data that the first author mis-interpreted. The second through fifth authors issued a complete retraction of the article, the findings, and all interpretations of the data. The original first author does not co-sign the retraction.

What does all of this mean?? Drama, serious drama. It seems the first author was very liberal in his/her data generation, analysis, and/or interpretation. In other words, this smells a bit like academic dishonesty. Obviously, someone was running some new tests and realized that the new information wasn’t jiving with the previous info published 2 years ago. So, they did a double check. They pulled up all of the old data and ran it again. And I bet they ran it a few times more and perhaps asked other people to look over the data, too.

In science, integrity matters. Other scientists will read your work and study your technique for his/her own research. Policy makers and others will likely use the information to make decisions.

Therefore, it is imperative to present your data as honestly as you can. Most scientists I know are very meticulous and very obsessed with making sure everything they do and report is accurate, precise, and honest. You don’t report findings that you simply did not find. You don’t invent data. You don’t invent subjects. You don't clone data (copy and paste the exact same data that may have been legitimately collected so that your sample size looks larger than what it is). These are no no’s. Usually, co-authors, graduate students, and in-house and funding oversight committees keep their eyes and ears open for such rats.

But there is also a process called peer-review and critique. Scientists share their ideas and work with many people. Critique is the nature of how we do and learn things. We look for holes, gaps, and weak spots. We point them out to each other and often recommend or help to patch them up. After all, science is an endeavor to learn more about our natural world. This retraction is a part of that process. Science is about updating our knowledge as we discover new things.

Deciphering the Science in Science News Reports

Breast cancer is not linked to abortion. That’s the science news story of note. This is a very interesting story. It’s another example of what we know about our bodies and hopefully it can help us make better decisions about our health and well-being.
But exactly how is this news discovered? HOW did this research team come to this conclusion? How do we KNOW?
Well, the answer lies in people’s understanding and perception of what science is. It has everything to do with understanding Scientific Processes. But learning about Scientific Processes can’t be achieved in a single sitting, but here’s a start. This news story presents a perfect opportunity to point out three key scientific processes.
a) Science discovery starts with a question.
b) Science experiments are designed to be fair and objective.
c) Many observations must be made to draw a fair conclusion.

a) Science discovery starts with a question.

Science is a human endeavor to gain knowledge about the natural world. Asking questions about important and interesting phenomena is the first step. Scientists don’t sit around postulating statements about the world. In fact, scientists ask more questions than we answer. It seems obvious that this team of researchers had the following questions in mind: Is there link between abortion and breast cancer? How does having an abortion affect a woman’s risk of developing breast cancer? Are women more likely to be diagnosed with breast cancer if they had an abortion sometime in their past?

b) Science experiments are designed to be fair and objective.

To answer these questions, the research team had to set up an experiment. However, researchers take care in designing an experiment that doesn’t tilt the results in one direction or the other. Science provides a way for people to learn more about the natural world by investigating a question thoroughly and methodologically. Experiments must be able to yield clear and objective answers that answer only the question at hand. Previous studies were biased because they only studied women who were already confirmed to have breast cancer. A fair experiment would involve studying women who were healthy to begin with and then see if breast cancer develops. Another thing to do would be to make sure that the supposed link to breast cancer isn’t just about an early-ending pregnancy. So the researchers also included women whose pregnancies ended involuntarily due to miscarriage.

c) Many observations must be made to draw a fair conclusion

In research, sample size matters. This study tracked over 100,000 women for 10 years. Having a large sample size demonstrates that this team expended a lot of effort to really searching for the relationship between abortion/miscarriage and breast cancer. If the studied was based only on 10 women, this would signal to me that the researchers didn’t really thoroughly and fully examine the question. By having a larger number of subjects, it demonstrates that researchers spent a lot of time and energy searching for the relationship between abortion/miscarriage and breast cancer. A study based on a larger sample size has results that are more trustworthy than the results of a study based on a smaller sample size.

A news release about the Breast Cancer and Abortion study can be accessed here. The original article published in a medical journal can be accessed here.