The Nature of Science

Showing posts with label Biology. Show all posts

We Are Stardust

Helena Curtis was an amazing writer. She's famous for her introductory biology textbook published by Worth beginning in 1968 [Good Science Writers: Helena Curtis]. Here's the opening paragraphs.

Our universe began, according to current theory, with an explosion that filled all space, with every particle of matter hurled away from every other particle. The temperature at the time of the explosion—some 10 to 20 billion years ago—was about 100,000000000 degrees Celsius (10¹¹ °C). At this temperature, not even atoms could hold together; all matter was in the form of subatomic, elementary particles. Moving at enormous velocities, even those particles had fleeting lives. Colliding with great force, they annihilated one another, creating new particles and releasing great energy.

As the universe cooled, two types of stable particles, previously present only in relatively small amounts, began to assemble. (By this time, several hundred thousand years after the "big bang" is believed to have taken place, the temperature had dropped to a mere 2500°C, about the temperature of white-hot wire in an incandescent light bulb.) These particles—protons and neutrons—are very heavy as subatomic particles go. Held together by forces that are still incompletely understood, they formed the central cores, or nuclei, of atoms. These nuclei, with their positively charged protons, attracted small, light, negatively charged particles—electrons—which moved rapidly around them. Thus, atoms came into being.

It is from these atoms—blown apart, formed, and re-formed over the course of several billion years—that all the stars and planets of our universe are formed, including our particular star and planet. And it is from the atoms present on this planet that living systems assembled themselves and evolved. Each atom in our own bodies had its origin in that enormous explosion 10 to 20 billion years ago. You and I are flesh and blood, but we are also stardust.

Neil DeGrasse Tyson tops that in his spontaneous answer to the question, "What is the most astounding fact you can share with us about the Universe?"

If you're going to sing "we are stardust" then you can't do it any better than this group. The song was written by Joni Mitchell (another Canadian) but her version is not as good.

[Hat Tip: Phil Plait of Bad Astronomy: Neil Tyson’s most astounding fact.]

These are not berries!

This is Juniperus communis from Botany Photograph of the Day. If you visit that website you'll learn two three things about juniper that you didn't know before: (1) juniper grows in lots of places, (2) the "berries" aren't berries, (3) gin comes from the French word for juniper.

Core Concepts: Evolution

The AAAS document, Vision and Change in Undergraduate Biology Education, defines five core concepts for biological literacy. Evolution is at the top of the list, right where it belongs.

1. EVOLUTION:

The diversity of life evolved over time by processes of mutation, selection, and genetic change. Darwin’s theory of evolution by natural selection was transformational in scientists’ understanding of the patterns, processes, and relationships that characterize the diversity of life. Because the theory is the fundamental organizing principle over the entire range of biological phenomena, it is difficult to imagine teaching biology of any kind without introducing Darwin’s profound ideas. Inheritance, change, and adaptation are recurring themes supported by evidence drawn from molecular genetics, developmental biology, biochemistry, zoology, agronomy, botany, systematics, ecology, and paleontology. A strong preparation in the theory of evolution remains essential to understanding biological systems at all levels.

Themes of adaptation and genetic variation provide rich opportunities for students to work with relevant data and practice quantitative analysis and dynamic modeling. Principles of evolution help promote an understanding of natural selection and genetic drift and their contribution to the diversity and history of life on Earth. These principles enable students to understand such processes as a microbial population’s ability to develop drug resistance and the relevance of artificial selection in generating the diversity of domesticated animals and food plants.

I would have written a different description—one that placed emphasis on Darwin's contribution but did not imply that his views represent modern evolutionary theory. I would also have mentioned genetics, especially population genetics, as the key to understanding modern evolution.

Nevertheless, one can't argue that evolution is the number one core concept in the biological sciences. Are we teaching it correctly in undergraduate courses. No, we are not. Are we teaching it enough in our undergraduate courses? No, again.

I think the main problem was completely ignored by the committee that drew up this document. The problem is that most professors don't understand evolution well enough to integrate this core concept into their courses. It's not enough for everyone to agree that evolution is a core concept. You also have to understand the core concept in order to teach it properly.

I see evidence in the description above suggesting that even the committee members were fuzzy on the core concept. What, for example, is "the theory of evolution"?

Vision & Change in Undergraduate Biology Education: Bruce Alberts

The American Association for the Advancement of Science (AAAS) has published a document called Vision and Change in Undergraduate Biology Education. Over the next few days I'm going to introduce the main recommendations and hopefully stimulate some discussion.

Today, we'll start with a video from Bruce Alberts the former head of the National Academies and currently editor-in-chief of Science magazine (published by AAAS). Pay attention to what he has to say. I agree with everything.¹

Bruce Alberts understands that we (university professors) are the problem and it's up to us to fix it.

... the future of science education ... depends on what college professors do in their teaching much more than I would ever have expected ...

Dr. Bruce Alberts’ Message to Vision and Change

1. Bruce was my Ph.D. supervisor.

Why Has this Bee Landed on this Flower?

This is a photo from Botany Photo of the Day. The flower is Crepis barbigera.

Why is the bee visiting this flower? What is the evolutionary advantage of attracting bees? You may think you know the answer but you will be surprised by the comment at the bottom of the posting on the Botany Photo of the Day website. Nothing in biology is simple.

Bacteria Fossils in Meteorites

When I first heard about the discovery of fossil bacteria in meteorites I immediately read the paper in the Journal of Cosmology [Fossils of Cyanobacteria in CI1 Carbonaceous Meteorites: Implications to Life on Comets, Europa, and Enceladus]. The first thing I noticed was that this "journal" seemed to be of very low quality. A little bit of digging revealed that it was some sort of online journal that publishes just about everything.

The second thing I noticed was that the evidence of fossils in these meteorites was not convincing. It seemed like the author, Richard B. Hoover, was not being very skeptical about what he was seeing. I dismissed the paper, it was almost certainly not true.

Lot's of other people reached the same conclusion.

Ian Musgrove at The Panda's Thumb [Life from Beyond Earth on a Meteorite, or Pareidolia?] [Commentaries posted at Journal of Cosmology]

Phil Plait at Bad Astronomy [Followup thoughts on the meteorite fossils claim]

PZ Myers at Pharyngula [Did scientists discover bacteria in meteorites?]

Rosie Redfield at RRResearch [Is this claim of bacteria in a meteorite any better than the 1996 one?]

The Journal of Cosmology has now published 21 commentaries on the paper and only two of them are the least bit critical or skeptical of the results. That inspired the journal to insert this statement in the introduction to the article.

Official Statement The Journal of Cosmology,
Have the Terrorists Won?
Only a few crackpots and charlatans have denounced the Hoover study. NASA's chief scientist was charged with unprofessional conduct for lying publicly about the Journal of Cosmology and the Hoover paper. The same crackpots, self-promoters, liars, and failures, are quoted repeatedly in the media. However, where is the evidence the Hoover study is not accurate?

Few legitimate scientists have come forward to contest Hoover's findings. Why is that? Because the evidence is solid.

But why have so few scientists come forward to attest to the validity? The answer is: They are afraid. They are terrified. And for good reason.

The status quo and their "hand puppets" will stop at nothing to crush debate about important scientific issues, and this includes slander, defamation, trade libel... they will ruin you. Three hundred years ago, they would burn you for questioning orthodoxy. Has anything changed?

The scientific community must march according to the tune whistled by those who control the funding. If you don't do as you are told, if you dare to ask the wrong questions, they will destroy you.

JOC offered the scientific community a unique opportunity to debate an important paper, but for the most part they have declined.

The message is: Be afraid. Be very afraid. Or you will be destroyed.

Why is America in decline?

Maybe the terrorists have won.

Did you need convincing that this is not real science?

Now here's the tough question. Why did so many people immediately see that this paper was flawed while many others, including some journalists, were taken in? I think it's because many of us recognized this as an extraordinary claim that required extraordinary evidence. We also realized that if this was even close to being true it would be published as a front page story in Science or Nature. In addition, we have lived through many examples of exaggerated claims, including previous claims of meteorite fossils that proved to be untrue; not to mention the 3.5 billion year old fossils that weren't fossils [Did Life Arise 3.5 Billion Years Ago?].

It's a combination of skepticism and experience. Can that be taught?

Astronomy and Biology

This is a remarkable picture. Depending on your personal preferences, you may be attracted to the sky in the background or the beautiful blue color along the shoreline of the lake. Are you an astronomer or a biologist, or both?

Phil took the picture and he explains it at: Gippsland Lakes.

Hat Tip: another Phil at Bad Astronomy

Lies, Damned Lies, and Medical Science

Here's an article from the Atlantic that everyone should read: Lies, Damned Lies, and Medical Science. It highlights the efforts of John Ioannidis to discover what's true and what's not true about modern medical research publications and clinical trials. I think this is going to become one of the hottest topics in science within a few years. The fallout will be horrendous when the public realizes that doctors are not as scientific as we thought.

Some interesting quotes from the article should prompt you to follow the link to the Atlantic website.

It didn’t turn out that way. In poring over medical journals, he was struck by how many findings of all types were refuted by later findings. Of course, medical-science “never minds” are hardly secret. And they sometimes make headlines, as when in recent years large studies or growing consensuses of researchers concluded that mammograms, colonoscopies, and PSA tests are far less useful cancer-detection tools than we had been told; or when widely prescribed antidepressants such as Prozac, Zoloft, and Paxil were revealed to be no more effective than a placebo for most cases of depression; or when we learned that staying out of the sun entirely can actually increase cancer risks; or when we were told that the advice to drink lots of water during intense exercise was potentially fatal; or when, last April, we were informed that taking fish oil, exercising, and doing puzzles doesn’t really help fend off Alzheimer’s disease, as long claimed. Peer-reviewed studies have come to opposite conclusions on whether using cell phones can cause brain cancer, whether sleeping more than eight hours a night is healthful or dangerous, whether taking aspirin every day is more likely to save your life or cut it short, and whether routine angioplasty works better than pills to unclog heart arteries.

Still, Ioannidis anticipated that the community might shrug off his findings: sure, a lot of dubious research makes it into journals, but we researchers and physicians know to ignore it and focus on the good stuff, so what’s the big deal? The other paper headed off that claim. He zoomed in on 49 of the most highly regarded research findings in medicine over the previous 13 years, as judged by the science community’s two standard measures: the papers had appeared in the journals most widely cited in research articles, and the 49 articles themselves were the most widely cited articles in these journals. These were articles that helped lead to the widespread popularity of treatments such as the use of hormone-replacement therapy for menopausal women, vitamin E to reduce the risk of heart disease, coronary stents to ward off heart attacks, and daily low-dose aspirin to control blood pressure and prevent heart attacks and strokes. Ioannidis was putting his contentions to the test not against run-of-the-mill research, or even merely well-accepted research, but against the absolute tip of the research pyramid. Of the 49 articles, 45 claimed to have uncovered effective interventions. Thirty-four of these claims had been retested, and 14 of these, or 41 percent, had been convincingly shown to be wrong or significantly exaggerated. If between a third and a half of the most acclaimed research in medicine was proving untrustworthy, the scope and impact of the problem were undeniable. That article was published in the Journal of the American Medical Association.

[Hat Tip, again to John Wilkins]

Astigmata

Today's taxon of the week at Catalogue of Organisms is Astigmata [Life in the Fast Lane]. If you think you're not familiar with astigmata then get on over to Christopher Taylor's blog and correct that false assumption.

Advertising 23andMe

Some bloggers are huge fans of genetic testing. They frequently post articles promoting one of the private companies that charge you for doing these tests. ScienceRoll recently posted this video of Anne Wojcicki making a pitch for her company. Wojcicki is one of the co-founders of 23andMe. It's interesting to see how she mixes various rationales for genetic testing with a pitch for 23andMe.

Imagine this was a talk by the CEO of a major pharmaceutical company about the importance of their drugs and why you should buy them. We would probably be more skeptical than we seem to be about Ann Wojcicki. Why is that?

Name This Tree

Seriously, what kind of tree is this? It grows in Belgium.

[Photo by Ms. Sandwalk]

Name These Geneticists

This is a collection of "geneticists" from the latest issue of Genetics (November 2009). How many can you identify? The correct answers are here.

The Cutest of all Invertebrates

Catalogue of Organisms features these cute little animals on "Taxon of the Week."

If you follow the link on that blog to a more detailed overview of the taxon you get a bonus—a description of why Christopher Taylor didn't make it to the International Conference of Arachnology in Brazil.

The Problem of Race .... Again

The current politically correct view of human races is that they don't exist. Surprisingly, this view has been adopted by many scientists, including biologists, who should know better.

Bruce T. Lahn and Lanny Ebenstein have published an opinion piece in this week's issue of Nature. Everyone should read it [Let's celebrate human genetic diversity].

They begin by pointing out the problem and then they state their position.

The current moral position is a sort of 'biological egalitarianism'. This dominant position emerged in recent decades largely to correct grave historical injustices, including genocide, that were committed with the support of pseudoscientific understandings of group diversity. The racial-hygiene theory promoted by German geneticists Fritz Lenz, Eugene Fischer and others during the Nazi era is one notorious example of such pseudoscience. Biological egalitarianism is the view that no or almost no meaningful genetically based biological differences exist among human groups, with the exception of a few superficial traits such as skin colour3. Proponents of this view seem to hope that, by promoting biological sameness, discrimination against groups or individuals will become groundless.

We believe that this position, although well-intentioned, is illogical and even dangerous, as it implies that if significant group diversity were established, discrimination might thereby be justified. We reject this position. Equality of opportunity and respect for human dignity should be humankind's common aspirations, notwithstanding human differences no matter how big or small. We also think that biological egalitarianism may not remain viable in light of the growing body of empirical data (see box).

These guys seem to be a bit late in realizing that the scientific data doesn't support the politically correct "biological egalitarianism" viewpoint but, as they say, better late than never.

Here's their bottom line.

Promoting biological sameness in humans is illogical, even dangerous
To ignore the possibility of group diversity is to do poor science and poor medicine
A robust moral position is one that embraces this diversity as among humanity's great assets

Bravo! I'm glad that more and more scientists are speaking out on this issue.

Lahn, B.T. and Ebenstein, L. (2009) Let's celebrate human genetic diversity. Nature 461:726-728 [Nature]

[Hat Tip: Nils Reinton at BIOpinionated: I Wish I Wrote This (me too! -LAM)]

UCSC Official Mascot

Fred Zlotnick took this picture of a banana slug in his back yard.

Believe it or not, the banana slug is the official mascot of the University of California Santa Cruz.

The Banana Slug, a bright yellow, slimy, shell-less mollusk found in the campus's redwood forest, was the unofficial mascot for UC Santa Cruz's coed teams since the university's early years. The students' adoption of such a lowly creature for a team mascot was their reaction to the fierce athletic competition fostered at most American universities. UCSC has always offered a wide-ranging physical education and recreation program designed to appeal to the greatest number of students, but it has based its approach on some unusual ideas: that athletics are for all students, not just team members of major sports; that the most important goal of a collegiate physical education department should be to introduce as many students as possible to lifelong physical activities; and that the joy of participating is more important than winning.

In 1980, when some campus teams wanted more organized yet still low-key participation in extramural competition, UCSC joined Division III of the NCAA in five sports. Since the application required an official team name, UCSC's then chancellor polled the student players, and out of this small group emerged a consensus for a new moniker--the sea lions. It was a choice that the chancellor considered more dignified and suitable to serious play than the Banana Slugs. But the new name did not find favor with the majority of students, who continued to root for the Slugs even after a sea lion was painted in the middle of the basketball floor.

After five years of dealing with the two-mascot problem, an overwhelming proslug straw vote by students in 1986 convinced the chancellor to make the lowly but beloved Banana Slug UCSC's official mascot. By the time the chancellor had left office, he was won over to the proslug camp, even to the point of featuring the Slug on his personal holiday card.

In May 2004, Reader's Digest named the Banana Slug the best college mascot. The Banana Slug even figured in a court case involving campus mascots. Judge Terence Evans, writing the opinion for the Seventh Circuit Court of Appeals, stated the following: "We give the best college nickname nod to the University of California, Santa Cruz. Imagine the fear in the hearts of opponents who travel there to face the imaginatively named 'Banana Slugs'?" (Crue et al. v. Aiken, June 1, 2004)

Our Sammy the Slug mascot has been appearing around campus at sports events and other functions. And, when the men's tennis team played in the NCAA championships, their T-shirts read: "Banana Slugs-No Known Predators."

UC Santa Cruz Foundation trustee Anne Neufeld Levin wrote a children's book, Sally Slug, illustrated by UCSC alumna and former Foundation trustee Patricia Rebele. The book, published in 2002, is available at slugstore.ucsc.edu. Proceeds from sales of the book benefit the UCSC Foundation and provide for art history purchases and exhibits in the library.

Sounds like my kind of school. I wonder if they need a biochemistry Prof?

Land Snails and Slugs

Most of us don't know very much about slugs and land snails but Christopher Taylor at Catalogue of Organisms is doing his best to educate us (and himself): Wild Slug Chases (Taxon of the Week: Gastrodontoidea).

I need to warn you that his posting isn't suitable for all audiences. Some of these animals are capable of having sex with themselves and that's not something you want your children to know. Also, some of these animals aren't as pretty as warm fuzzy animals like cats. I find it helps to think of snails and slugs as dinner rather than pets.¹

1. For some people, this works for cats too.

Oenothera californica subsp. eurekensis

This is a photo of the rare, endangered, Eureka Dunes evening primrose. Read about it on Botany Photo of the Day.

How Many People Have a Tape Worm Named After Them?

How many people have a tape worm named after them? Quite a few, as it turns out.

Do you know any of these people? Yes [A Tapeworm To Call My Own].

Ugh!

Taxonomic Inflation

The number of new species discovered is growing every year, although we often hear more about threatened extinctions. In many cases this is because of new observations leading to the identification of new species. For the most part, these are not entirely new organisms—they are species that are closely related to existing species.

Given the ongoing battles between lumpers and splitters in the taxonomic community, one wonders whether the discovery of new species isn't just due to the elevation of varieties to the level of species. For example, there are many varieties of giraffe and some people propose that the current species, Giraffa camelopardalis, should be split into several species. This depends on your definition of species.

Christopher Taylor of Catalogue of Organisms reviews a recent paper that addresses the problem [Keeping an Eye on Inflation]. Turns out that the recent redefinition of species doesn't correlate with the increase in splitting so that doesn't seem to explain taxonomic inflation.

Unfortunately Chris doesn't answer the most important questions.

Is it true that God has an inordinate fondness for beetles or is it just overzealous insect taxonomists?

If you split G. camelopardalis then why not split Homo sapiens as well?

The Debut of Science Nation

Science Nation is an online magazine produced by the National Science Foundation (USA). The first "issue" was published yesterday.

Before looking at it, let's see why this is happening.

In the National Science Foundation's Science Nation online magazine, we examine the breakthroughs, and the possibilities for new discoveries about our planet, our universe and ourselves: An artifical retina that can help the blind to see; new materials to build things bigger, better, lighter, and stronger; new ways to make our lives better without making the environment worse; and what we can learn from organisms that can live and thrive in frozen deserts or steaming-hot volcanic vents. Each week, Science Nation takes a dynamic, entertaining look at the research--and the researchers-- that will change our lives.

That's not very helpful. The motivation seems to be to promote NSF by reaching out directly to the general public—"The online magazine that's all about science for the people." I guess NSF wants to publicize work that it's funding. Maybe it wants to contribute to science education?

The first video is called Extremophile Hunter. It highlights the work of Richard Hoover who looks for bacteria that live in extremely cold environments. Hoover also believes that life may have originated in other planets and was brought to Earth on meteorites.

To test that theory, he cracks open so-called carbonaceous meteorites, which are the remains of cometary debris or water-bearing asteroids that have hit the Earth. Being careful to avoid contamination, he examines their insides with an electron microscope.

"They are older than the planet Earth, which is accepted at being 4.5 billion years old," said Hoover. "So I like to say these carbonaceous meteorites are actually older than dirt!"

Some of the structures he has imaged from these meteorites are intriguing, bearing striking similarities to bacteria here on Earth. Could these be the fossilized remains of extraterrestial life?

"I am convinced that what I am finding in the carbonaceous meteorites are in many cases biological in nature, and I think they are indigenous and not terrestrial contaminants," said Hoover.

It is a highly controversial interpretation.

"We have for a long time thought that all life, as we know it, originated on Earth. And there isn't any life anywhere else," he said. "That's an idea, it's a hypothesis, it's a totally unproven hypothesis."

Hoover hopes his work will help get at the truth, whatever that may be. And as interplanetary probes become more sophisticated, scientists may eventually turn up a biological sample for examination. Then we'll know if life out there looks anything like it does here.

The National Science Foundation goes on record supporting the idea that traces of extraterrestrial life have been detected in "so-called carbonaceous" meteorites that are older than the Earth. Yes, they admit that the idea is "controversial" but what message is being conveyed to the general public? Is it the message that the vast majority of scientists dismiss these "imaged structures" as artifacts?

I've been critical of science journalism for not doing a good job of reporting science. I've also been critical of scientists for not doing a good job of doing science properly—making the job of science journalists that much harder. Now we have a scientific funding agency taking on the role of science journalism. One might expect that the number one criterion of science journalism; namely, scientific accuracy, would be ensured. It's disappointing to see that scientific accuracy is the first casualty in the first episode of Science Nation. It was sacrificed on the alter of media hype.