Tag Archives: scientific inquiry

Gravity and the Scientific Method

One of the topics I return to repeatedly is the scientific method – theories must to tested. As evidence mounts that new ideas do a good job of explaining theories they become more accepted. But they continue to be tested in new ways as the ideas are extended and ramification are explored. And science progress means that old conventions can be overturned as new evidence is gathered.

Science is not about current beliefs. Science is about seeking knowledge. If the search for knowledge leads to evidence that old ideas were wrong those ideas are overturned. Since people are involved that process isn’t as clean as it sounds above. People get comfortable with beliefs. They build careers on expanding those beliefs. Most are uncomfortable when they are challenged and don’t accept new ideas even when the evidence mounts. But some do accept the new ideas. Some challenge the new ideas by running experiments. And some of those prove the new ideas faulty. Some become convinced of the new ideas as the results of their experiments make the new ideas seem more sensible (instead of getting the results they expected).

Building the body of scientific knowledge is not nearly as clean and simple as most people think. It isn’t a simple process, what is the underlying truth can be debatable. But the beauty of the scientific process is how it helps us overcome our biases and provide evidence to support the theories we support. The scientific method (combined with our human involvement) doesn’t mean new ideas are accepted easily but it does mean new ideas compete on the basis of evidence not just the power of those that hold the beliefs.

Is gravity not actually a force? Forcing theory to meet experiments
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New Analysis of Primordial Soup Experiment Half a Century Later

Open access paper: Primordial synthesis of amines and amino acids in a 1958 Miller H₂S-rich spark discharge experiment

Archived samples from a previously unreported 1958 Stanley Miller electric discharge experiment containing hydrogen sulfide (H₂S) were recently discovered and analyzed using high-performance liquid chromatography and time-of-flight mass spectrometry. We report here the detection and quantification of primary amine-containing compounds in the original sample residues, which were produced via spark discharge using a gaseous mixture of H₂S, CH₄, NH₃, and CO₂. A total of 23 amino acids and 4 amines, including 7 organosulfur compounds, were detected in these samples.

The major amino acids with chiral centers are racemic within the accuracy of the measurements, indicating that they are not contaminants introduced during sample storage. This experiment marks the first synthesis of sulfur amino acids from spark discharge experiments designed to imitate primordial environments. The relative yield of some amino acids, in particular the isomers of aminobutyric acid, are the highest ever found in a spark discharge experiment.

The simulated primordial conditions used by Miller may serve as a model for early volcanic plume chemistry and provide insight to the possible roles such plumes may have played in abiotic organic synthesis. Additionally, the overall abundances of the synthesized amino acids in the presence of H₂S are very similar to the abundances found in some carbonaceous meteorites, suggesting that H₂S may have played an important role in prebiotic reactions in early solar system environments.

11 Year Old Using Design of Experiments

This reminds me of great times I had experimenting with my father when I was a kid. Though, to be honest, Sarah is much more impressive than I was.

Catapulting to Success with Design of Experiments

Sarah Flexman with her trebuchet at the Storm the Castle science challenge in North Carolina.

At the end of 2010, Sarah had decided to take part in Storm the Castle, one of the events offered in the statewide science Olympiad competition. This particular challenge was to design, build and launch a model trebuchet, which is a medieval-style catapult for hurling heavy stones…

Here’s Sarah’s whole process: She built the trebuchet, tested it, used JMP for DOE during optimization, changed the hook angle and sling to improve performance, did more tests, entered this new data, reran the model, and made her final prediction graphs. The variables in her DOE were string length, counterweight and projectile weight, and she optimized for distance – that is, how far the projectile would go.

“Rather than doing 125 tests because we have three variables with five levels each, DOE found a way for us to perform only 26 tests and get approximately the same results. I typed in the results, ran the model and used the JMP Profiler. I understood how the variables predicted the outcome and found several patterns,” she explained.
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“I hadn’t done any building like that. The whole day was fun. It was a very open learning environment. You were experimenting with things you had never done before. I would definitely do it again,” Sarah said. And she will – next year.

I have collected quite a few design of experiments resources, for those who are interested in learning more. Here is a nice webcast by brother: Combinatorial Testing – The Quadrant of Massive Efficiency Gains, discussing the incredibly efficiency designed combinatorial testing (very similar ideas to design of experiments) can provide.

Diet May Help ADHD Kids More Than Drugs

Kids with ADHD can be restless and difficult to handle. Many of them are treated with drugs, but a new study says food may be the key. Published in The Lancet journal, the study suggests that with a very restrictive diet, kids with ADHD could experience a significant reduction in symptoms.

The study’s lead author, Dr. Lidy Pelsser of the ADHD Research Centre in the Netherlands, writes in The Lancet that the disorder is triggered in many cases by external factors — and those can be treated through changes to one’s environment. “ADHD, it’s just a couple of symptoms — it’s not a disease,” the Dutch researcher tells All Things Considered weekend host Guy Raz.

The way we think about — and treat — these behaviors is wrong, Pelsser says. “There is a paradigm shift needed. If a child is diagnosed ADHD, we should say, ‘OK, we have got those symptoms, now let’s start looking for a cause.’ ”
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According to Pelsser, 64 percent of children diagnosed with ADHD are actually experiencing a hypersensitivity to food. Researchers determined that by starting kids on a very elaborate diet, then restricting it over a few weeks’ time. “It’s only five weeks,” Pelsser says. “If it is the diet, then we start to find out which foods are causing the problems.”

Teachers and doctors who worked with children in the study reported marked changes in behavior. “In fact, they were flabbergasted,” Pelsser says.

Evidence of Extraterrestrial Life Discovered?

Has evidence of extraterrestrial life been discovered? In Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites , Richard B. Hoover, Ph.D. NASA/Marshall Space Flight Center, puts forth his evidence on the discovery of evidence of cyanobacteria in meteorites.

Dr. Hoover has discovered evidence of microfossils similar to Cyanobacteria, in freshly fractured slices of the interior surfaces of the Alais, Ivuna, and Orgueil CI1 carbonaceous meteorites. Based on Field Emission Scanning Electron Microscopy (FESEM) and other measures, Dr. Hoover has concluded they are indigenous to these meteors and are similar to trichomic cyanobacteria and other trichomic prokaryotes such as filamentous sulfur bacteria. He concludes these fossilized bacteria are not Earthly contaminants but are the fossilized remains of living organisms which lived in the parent bodies of these meteors, e.g. comets, moons, and other astral bodies. The implications are that life is everywhere, and that life on Earth may have come from other planets.

The importance of this claim is hard to ignore. The journal includes a statement from Dr. Rudy Schild, Center for Astrophysics, Harvard-Smithsonian, Editor-in-Chief, Journal of Cosmology:

Dr. Richard Hoover is a highly respected scientist and astrobiologist with a prestigious record of accomplishment at NASA. Given the controversial nature of his discovery, we have invited 100 experts and have issued a general invitation to over 5000 scientists from the scientific community to review the paper and to offer their critical analysis. Our intention is to publish the commentaries, both pro and con, alongside Dr. Hoover’s paper. In this way, the paper will have received a thorough vetting, and all points of view can be presented. No other paper in the history of science has undergone such a thorough analysis, and no other scientific journal in the history of science has made such a profoundly important paper available to the scientific community, for comment, before it is published. We believe the best way to advance science, is to promote debate and discussion.

Read the full paper.

The filaments have been observed to be embedded in freshly fractured internal surfaces of the stones. They exhibit features (e.g., the size and size ranges of the internal cells and their location and arrangement within sheaths) that are diagnostic of known genera and species of trichomic cyanobacteria and other trichomic prokaryotes such as the filamentous sulfur bacteria. ESEM and FESEM studies of living and fossil cyanobacteria show similar features in uniseriate and multiseriate, branched or unbranched, isodiametric or tapered, polarized or unpolarized filaments with trichomes encased within thin or thick external sheaths. Filaments found in the CI1 meteorites have also been detected that exhibit structures consistent with the specialized cells and structures used by cyanobacteria for reproduction (baeocytes, akinetes and hormogonia), nitrogen fixation (basal, intercalary or apical heterocysts) and attachment or motility (fimbriae).
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These studies have led to the conclusion that the filaments found in the CI1 carbonaceous meteorites are indigenous fossils rather than modern terrestrial biological contaminants that entered the meteorites after arrival on Earth. The Î´13C and D/H content of amino acids and other organics found in these stones are shown to be consistent with the interpretation that comets represent the parent bodies of the CI1 carbonaceous meteorites. The implications of the detection of fossils of cyanobacteria in the CI1 meteorites to the possibility of life on comets, Europa and Enceladus are discussed.

Has life been found in a meteorite? by Phil Plait
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Red-light Cameras Save Lives, Could Save More if Used in More Cities

Red light cameras saved 159 lives in 2004-08 in 14 of the biggest US cities, a new analysis by the Insurance Institute for Highway Safety shows. Had cameras been operating during that period in all large cities, a total of 815 deaths would have been prevented.

“The cities that have the courage to use red light cameras despite the political backlash are saving lives,” says Institute president Adrian Lund. The researchers found that in the 14 cities that had cameras during 2004-08, the combined per capita rate of fatal red light running crashes fell 35 percent, compared with 1992-96. The rate also fell in the 48 cities without camera programs in either period, but only by 14 percent.

The rate of all fatal crashes at intersections with signals — not just red light running crashes — fell 14 percent in the camera cities and crept up 2 percent in the noncamera cities. In the camera cities, there were 17 percent fewer fatal crashes per capita at intersections with signals in 2004-08 than would have been expected. That translates into 159 people who are alive because of the automated enforcement programs.

This result shows that red light cameras reduce not only fatal red light running crashes, but other types of fatal intersection crashes as well. One possible reason for this is that red light running fatalities are undercounted due to a lack of witnesses to explain what happened in a crash. Drivers also may be more cautious in general when they know there are cameras around.

Based on these calculations, if red light cameras had been in place for all 5 years in all 99 US cities with populations over 200,000, a total of 815 deaths could have been avoided.

“Somehow, the people who get tickets because they have broken the law have been cast as the victims,” Lund says. “We rarely hear about the real victims — the people who are killed or injured by these lawbreakers.” Red light running killed 676 people and injured an estimated 113,000 in 2009. Nearly two-thirds of the deaths were people other than the red light running drivers — occupants of other vehicles, passengers in the red light runners’ vehicles, bicyclists, or pedestrians.

Previous research has established that red light cameras deter would-be violators and reduce crashes at intersections with signals. Institute studies of camera programs have found that red light violations fell at intersections where cameras were installed and that this effect also spilled over to intersections without cameras. An Institute study in Oxnard, Calif., found that injury crashes at intersections with traffic signals fell 29 percent citywide after automated enforcement began.

The new study adds to this by showing that cameras reduce not only violations and crashes throughout entire communities but deaths, too.

Red-light cameras save lives, study says

The 2.2 million intersection crashes recorded in 2009 made up about 41 percent of all accidents. They resulted in 81,112 serious injuries and 7,358 deaths. Police established red-light running as the cause of 676 deaths and 113,000 injuries. The vast majority of the people who died – 64 percent – were not driving the vehicle that ran the light. They were passengers, other drivers, pedestrians and cyclists.

Naturally Curious Children

I write this blog because when I was a kid I was curious and had parents who gave me enough interesting answers and interesting resources to build on that curiosity. And I am still curious today. I love learning. And I love to hear about kids learning.

The Big Girl has worked out evolution

She was ecstatic when we ended up with a rooster in our ‘sexed’ chickens even though Mummy and Daddy weren’t too impressed, because she wants more little fluffy chicks. I think that counts as evidence she knows you need boys and girls to get babies.
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“What would happen if there were no boys?” This is the question she came out with the other day.

“Well, there would be no babies.” I didn’t quite get the problem seeing we were feeding the rather prolific guinea pigs at the time and we’ve been talking about separating them.
“But what if there were no boys at all? So no-one could have babies?”
“Eventually, they would all die.”
“But there wouldn’t be any left!”
“No, they would die out.”
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“How did humans start?”… a puzzled little crease in her forehead. “Because if there weren’t any around with the dinosaurs they must have started sometime. How could there be no humans and then they’re there? What was the Mummy?”
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“Well, they weren’t sudden. You know how you are a little bit different to Mummy and Daddy? That’s how it happened. The babies were just a little bit different to their parents and over a really, really long time they became people.”
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“But if there was only one it would die out.”
Well that came out of nowhere, did I miss half of this conversation?
“You know, the first person. It needs to have both a boy and a girl to have more people babies. So if there was only one it would die out.”
“Oh, from yesterday. Yes, you’re right. But people live in groups, so they’re all changing a tiny little bit at the same time.”

It is great to see developing minds at work. Exploring their natural curiosity. And taking in new information puzzling it out over time and then coming back to the ideas. This kind of curiosity is what drives learning and success.

8-10 Year Olds Research Published in Royal Society Journal

Eight-year-old children publish bee study in Royal Society journal

Their paper, based on fieldwork carried out in a local churchyard, describes how bumblebees can learn which flowers to forage from with more flexibility than anyone had thought. It’s the culmination of a project [Blackawton Bees] called ‘i, scientist’, designed to get students to actually carry out scientific research themselves.
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The class (including Lotto’s son, Misha) came up with their own questions, devised hypotheses, designed experiments, and analysed data. They wrote the paper themselves (except for the abstract), and they drew all the figures with colouring pencils.
It’s a refreshing approach to science education, in that it actually involves doing science.
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The children designed a Plexiglas cube with two entrances and a four-panelled light box in the middle. Each panel had 16 coloured lights, illuminated in clear patterns of blue and yellow. Each light had a feeder that dispensed either delicious sugar water or repulsive salty water. Once the bees had learned to drink from the feeders, the kids turned the lights on.

Absolutely great stuff. This is how to engage kids in science. Engage their inquisitive minds. Let them get involved. Let them experiment.

Some of the children’s questions when looking at what to discover using experiments:

What if… we could find out how much effort the bees will go through in order to get a reward? For instance, they have to move something heavy out of the way to get a reward.

What if… we could discover if bees can learn to go to certain colours depending on how sweet they are?

What if… we could find out how many colours they could remember?

And some of their comments:
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Scientific Inquiry: Arsenic for Phosphorus in Bacteria Cells

As would be expected with significant new scientific claims, scientists are examining the evidence. On her blog, Rosie Redfield, who runs a microbiology research lab in the Life Sciences Centre at the University of British Columbia, disputes NASA’s recent claims. This is how science is suppose to work. Scientists provide evidence. Other scientists review the evidence, try to verify the claims with experiments of their own and the scientific inquiry process moves toward new knowledge.

Arsenic-associated bacteria (NASA’s claims)

NASA’s shameful analysis of the alleged bacteria in the Mars meteorite made me very suspicious of their microbiology, an attitude that’s only strengthened by my reading of this paper. Basically, it doesn’t present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule).
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The authors then grew some cells with radioactive arsenate (73-As) and no phosphate, washed and dissolved them, and used extraction with phenol and phenol:chloroform to separate the major macromolecules. The protein fraction at the interface between the organic and aqueous phases had about 10% of the arsenic label but, because the interface material is typically contaminated with liquid from the aqueous phase, this is not good evidence that the cells’ protein contained covalently-bound arsenate in place of phosphorus. About 75% of the arsenic label was in the ‘supernatant ‘fraction. The authors describe this fraction as DNA/RNA, but it also contains most of the small water-soluble molecules of the cell, so its high arsenic content is not evidence that the DNA and RNA contain arsenic in place of phosphorus. The authors use very indirect evidence to argue that the distribution of arsenic mirrors that expected for phosphate, but this argument depends on so many assumptions that it should be ignored.
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I don’t know whether the authors are just bad scientists or whether they’re unscrupulously pushing NASA’s ‘There’s life in outer space!’ agenda. I hesitate to blame the reviewers, as their objections are likely to have been overruled by Science’s editors in their eagerness to score such a high-impact publication.

New claims have to provide strong evidence. time will tell if this discovery is actually a discovery. It will be amazing if it is, so I am pulling for it. But the story will need to have much more confirmation before we can be certain.

Arsenate-based DNA: a big idea with big holes

The study published in Science has a number of flaws. In particular, one subtle but critical piece of evidence has been overlooked, and it demonstrates that the DNA in question actually has a phosphate – not an arsenate -backbone.
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Wolfe-Simon et al. used a technique called nanoSIMS to analyze elemental concentrations of the agarose gel at the location of the DNA band. They determined that the part of the gel containing DNA also contained both arsenic and phosphorus. But what did they really analyze?

The answer is that the nanoSIMS determined the concentration of arsenic in the gel – not specifically in the DNA.
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Finally, there’s a simple experiment that could resolve this debate: analyze the nucleotides directly. Show a mass spectrum of DNA sequences demonstrating that nucleotides contain arsenate instead of phosphate. This is a very simple experiment, and would be quite convincing – but it has not been performed.

Changing Life as We Know It

Update: Independent researchers find no evidence for arsenic life in Mono Lake

NASA has made a discovery that changes our understanding of the very makeup of life itself on earth. I think my favorite scientific discipline name is astrobiology. NASA pursues a great deal of this research not just out in space but also looking at earth based life. Their astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

Felisa Wolfe-Simon processing mud from Mono Lake to inoculate media to grow microbes on arsenic.

Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur are the six basic building blocks of all known forms of life on Earth. Phosphorus is part of the chemical backbone of DNA and RNA, the structures that carry genetic instructions for life, and is considered an essential element for all living cells.

Phosphorus is a central component of the energy-carrying molecule in all cells (adenosine triphosphate) and also the phospholipids that form all cell membranes. Arsenic, which is chemically similar to phosphorus, is poisonous for most life on Earth. Arsenic disrupts metabolic pathways because chemically it behaves similarly to phosphate.

Researchers conducting tests in the harsh, but beautiful (see photo), environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.

“The definition of life has just expanded,” said Ed Weiler, NASA’s associate administrator for the Science Mission Directorate. “As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it.” This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth.

In science such huge breakthroughs are not just excepted without debate, however, which is wise.

Thriving on Arsenic:

In other words, every experiment Wolfe-Simon performed pointed to the same conclusion: GFAJ-1 can substitute arsenic for phosphorus in its DNA. “I really have no idea what another explanation would be,” Wolfe-Simon says.

But Steven Benner, a distinguished fellow at the Foundation for Applied Molecular Evolution in Gainesville, FL, remains skeptical. If you “replace all the phosphates by arsenates,” in the backbone of DNA, he says, “every bond in that chain is going to hydrolyze [react with water and fall apart] with a half-life on the order of minutes, say 10 minutes.” So “if there is an arsenate equivalent of DNA in that bug, it has to be seriously stabilized” by some as-yet-unknown mechanism.

It is sure a great story if it is true though. Other scientists will examine more data and confirm or disprove the claims.

“We know that some microbes can breathe arsenic, but what we’ve found is a microbe doing something new — building parts of itself out of arsenic,” said Felisa Wolfe-Simon, a NASA Astrobiology Research Fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., and the research team’s lead scientist. “If something here on Earth can do something so unexpected, what else can life do that we haven’t seen yet?”
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