Book Review: Two More Books about Polar Biomes

The two year celebration of research, discovery, and social studies of the globe’s Polar Regions comes to a close. International Polar Year 2007-2009 ends March 31st. Educators and Research teams from the around the world ramped up efforts to learn as much as we can about the ends of the earth before they are changed forever by climate change.
This will be my final book review dedicated to IPY.

Title: Scary Creatures of the Arctic
Author: Penny Clarke
Publisher: Scholastic

The Arctic is a very cold and windy place, but it is teeming with life. For thousands of years the plants, animals, and people have managed to get what they need from this harsh climate by paying attention to the patterns. Presenting a combination of photographs and illustrations the book shows us arctic landscapes, wildlife, and the people who live on top of the world and how they survive. This is a perfect introductory ecology book about this biome for third-fifth graders.

Title: Ookpik: The Travels of a Snowy Owl
Author: Bruce Hiscock
Publisher: Boyds Mills Press

The author recounts the life and aim to survive of an Ookpik, the Inuit word for snowy owl. This hardy species of owl lives all-year in the Arctic, hunting in open areas and in day light. But if food resources become limited they are known to migrate some seasons. They fly south to Canada and New England. This is the story of an ookpik who spent a winter in the Adirondack Mountains of upper state New York. Much to the delight of bird watchers, that owl spent the winter in a local town and farming community reaping the benefits of abundant mice, voles, hares, and small birds. It is a delightful book with beautiful watercolor illustrations.

Diversity in Science – Celebrating Women Achievers in Science.

The second installment of the Diversity in Science Carnival has been posted at Thus Spake Zuska. I am very happy so many people continue to participate in the effort. But can you believe it; I failed to write my post in time. However, I have a post-addendum contribution to Women Acheivers of STEM: Past and Present.

Today, I honor Dr. Roger Arliner Young. The name might sound masculine; she was indeed a woman, in fact the first African-American Woman to earn a doctorate in Zoology. While an unlikely undergraduate science student, she was mentored by Ernest Everett Just, a prominent Black zoologist at the turn-of-the-other-century and for anyone familiar with African-American Black Greek lettered organizations, a co-founder of Omega Psi Phi Fraternity, Inc.

Dr. Young’s story is interesting to me because I find myself particularly drawn to historical science leaders with whom I share an academic connection in this case an African-American woman who studied zoology. Her ground-breaking work was with paramecium and cells and in marine ecosystems. She is also the first African-American woman to publish in the journal Science. However, her scientific career was fraught with challenges. Her grades as an undergraduate student were unimpressive, but she was obviously brilliant. Her many mentors, prominent scientists at the time and white men saw past her grades and her life issues – she was caring for an invalid mother and had some mental instabilities. Initially she

was enrolled in the doctoral program at the University of Chicago (1929) – the same institution Charles Henry Turner attended. However, she failed her qualifying exams – an important exam in Ph.D. programs. She was embarrassed and disappeared. Years later, she re-surfaced taught at Howard University, her alma mater. However, things began to go sour there, too. She was dismissed from her position in 1937, but this time she turned the tables in her favor. She used the time to try for her Ph.D. again and was successful. She received her degree in 1940 from the University of Pennsylvania.

She continued to research and teach, but moved a lot from institution to institution. Eventually her mental distress got the best of her and was hospitalized. Though she never experienced any big fanfare and success, she is very much a real Woman Achiever and Science Hero of mine. Her life is a personal testimony that hardships are not permanent barriers. That even the most ‘unlikely’ students can sometimes possess impressive scientific minds. Science is staffed by real people, sometimes fragile people who live with their imperfect lives. I realize that my slowly moving dissertation meter and the life issues I confront daily are a part of life but it that doesn’t mean I can’t accomplish my goals. I sometimes feel a little sad for myself because I am the last of my cohort who has yet to graduate. Even students who started years after me have defended and moved away and I am still here. I feel lonely and disappointed. But then I think, yes, I’m still here. I’m sticking it out. Yes, it is taking me longer, much longer, to finish than I or any of my professors intended, but like Roger Arliner Young, I am finishing. And it doesn’t matter it how long it takes. It is her indomitable spirit that I channel today and everyday and I near completion of my dissertation; and when it is complete I will dedicate it to her memory.

Wordless Wednesdays: Mole Hills

Here is a sure sign of subtarrean life - soft mounds of dirt and mud means none other than moles!

Book Review: Ice Bears

International Polar Year is drawing to a close and I am still commemorating the occasion with posts dedicated to polar ecology.

Title: Ice Bears
Author: Brenda Z. Guiberson
Illustrator: Ilya Spirin
Publisher: Henry Holt and Company

So far, this book is my early favorite for the Outstanding Children’s Book Award in Animal Behavior for this year. The author accurately describes the behavior of polar bears, focusing on a mother-twin cubs unit. The illustrations supplement the narratives. I especially like how the author uses onomatopoeia to describe some of the animal behavior like nursing and vocalizations between mother cubs. Because of the endangered nature of this species, the book serves as a perfect example of how the fields of animal behavior, ecology, and conservation blend together to help us understand how species interact with each and their environment. And be sure to check out the Arctic Ice Report following the story proper. It summarizes the state of the polar bear and other polar animals to climate conditions of the arctic region. Ice is an important environmental condition that North Pole animals like the polar bear, seals, caribou, fish, and foxes require. The need each other and they all need the ice to survive.

It’s not too late to make your voice heard. Sign the Center for Biological Diversity’s petition to save the polar bear and bring awareness of the need to protect the habitat of other polar wildlife.

The cosmic "dark ages"

In brief, "dark ages" refers to the period after recombination occurred, about 380,000 years after the big bang, creating the cosmic microwave background (CMB), up to and partly including the time that the first stars had formed, perhaps as early as four hundred million years later, and caused the reionization of much of the neutral hydrogen in the universe.

That's a mouthful, but it's important to understand in order to have a useful discussion of the conditions that existed when the first stars and first galaxies in the universe formed. Many important open questions in astrophysics right now have to do with the nature of these events. Since I expect to discuss some of these questions, it's necessary to say some things about the "dark ages". That's what this note is about.

Let's start with the CMB. I'm going to give just a sketch. You might want to consult other references if you need more detail.

The period of time in which the CMB emerged is also known as the period of recombination. This was not an instantaneous process, but it did proceed relatively quickly, and is often thought of as a single event.

Basically, before recombination matter (mostly hydrogen and helium) and energy (light, i. e. photons) existed in thermal equilibrium. That is, the following reaction could occur with equal probability in either direction:

H + γ ⇄ p + e^-

Here, H stands for a hydrogen atom (with one electron), γ is a photon, p is a proton, and e^- is an electron. (We'll ignore helium, for simplicity.) What this formula says is that a photon of sufficient energy could dislodge an electron from a hydrogen atom to form a proton and a free electron, and with equal probability protons and free electrons could combine to form a hydrogen atom and a photon.

As the universe cooled after the big bang, the average temperature of the matter-energy plasma steadily dropped. Before the period of recombination, hydrogen atoms could exist, but not for very long, because most photons had enough energy to completely dislodge an electron, so the reaction went from left to right as often as from right to left.

Over a period of time lasting a few tens of thousands of years the situation changed so that most photons no longer had enough energy to dislodge an electron. (A low energy photon could still interact or "scatter" with a hydrogen atom by raising an electron to a higher energy level, but we can gloss over that detail.) Note that the average or "typical" photon energy may be a lot lower than what's needed to dislodge an electron, as long as there are still enough higher-energy photons around. This is a statistical situation governed by the Maxwell-Boltzmann equation, but all that really matters is that eventually photons and neutral hydrogen atoms "decouple" statistically.

So at some point you have recombination, when electrons combine with protons to make neutral hydrogen, and the process (mostly) doesn't reverse. Occasionally, a photon and a hydrogen atom may still interact, but as the universe expands, it's increasingly less likely for a photon and an atom to come close enough to interact, until the probability of interaction is essentially zero. This second stage is sometimes referred to as "decoupling" of matter and photons.

Thus the period of "dark ages" began right after the relatively brief process of recombination and decoupling. For simplicity, we date this point to a single time when the process was about half complete, roughly 380,000 years after the big bang.

This period is termed "dark", even though there were plenty of photons around, because there were as yet no stars or other compact sources of illumination. (There's another reasons for calling it "dark", which we'll get to in a moment.)

CMB photons have a nearly perfect black-body distribution. There is a clear peak of maximum energy in this distribution. What we observe is that this peak occurs at about 2 mm, in the microwave part of the spectrum. But the time of decoupling, 380,000 years after the big bang, corresponds to a redshift of z≈1100, so at the time of decoupling the peak photon energy was around a wavelength of just 2.2 μm (2200 nm) in the infrared part of the electromagnetic spectrum. (If you need to refresh your memory about how redshift works, check here.) So "dark" is not exactly the right term to use, but compared to abundant light from stars, it's not unreasonable.

After the time of recombination/decoupling, most hydrogen and helium atoms were neutral and un-ionized. This went on for several hundred million years. One of the most interesting open questions is about determining more exactly how long this lasted. We can reasonably guess what probably brought the dark ages to an end: formation of the first stars in the universe. But we don't have a good idea of just when this started, or how long the process took.

In this period, matter was beginning slowly to come together in higher-density clumps under the force of gravity. Dark matter, which outweighed ordinary matter then (as now), by a ratio of about 5.5:1 speeded up this process.

It was precisely this formation of regions of higher matter density that enabled the first stars to form. But because of this same higher density of matter around newborn stars, the abundant high-energy photons produced by these stars were again likely to interact with the nearby un-ionized matter, which scattered them and reduced their energy – dimming the light of these first stars.

One of the large uncertainties concerns the characteristics of this first generation of stars. We have no direct evidence about them. What we think we know about them is based on theoretical models rather than direct observation. (We discussed formation of the first stars back here.) However, it's widely believed that these stars were unlike stars formed later, right up to the present time. The first stars were probably quite large (maybe as much as 200 solar masses), very hot, and very bright. Because they burned their fuel so rapidly, their lifetimes would be very short, perhaps less than a million years.

Some of the light from extremely hot, massive stars such as those of the first generation is well into the ultraviolet part of the spectrum, around 90 nm. Such photons have an energy above 13.6 eV (91.2 nm wavelength), enough to completely ionize hydrogen. If these stars formed, say, 400 million years after the big bang, at a redshift of z≈11, the wavelength of their light would be shifted to the area beyond 1100 nm, which is in the infrared. That's beyond the range of human eyes, or most astronomical instruments. Consequently, we would have a very hard time detecting light from the first stars, even if they weren't so far away (over 13 billion light-years) and obscured by clouds of atomic hydrogen. That time period would still seem "dark" to us – there would be very little we could "see".

However, the first stars radiated so much energy, especially at ultraviolet wavelengths, that over time they effectively reionized all of the hydrogen in their vicinity. And this is (probably) what brought about the epoch of reionization in the universe, effectively ending the "dark ages".

The first stars were probably not part of galaxies, though we don't know for sure. If that's the case, they would be even harder to observe. The first objects we will be able to detect from this period almost certainly will be galaxies or quasars (which are galaxies with a very active central black hole). So the question of when galaxies began to form is separate, but equally puzzling. There is evidence that the first galaxies in fact did form before the end of the dark ages – because we can actually observe a few that show evidence of un-ionized hydrogen.

What we can say for sure is that the first stars must have consisted only of the primordial elements hydrogen and helium, since heavier elements (except for a small trace of lithium) formed and dispersed only when the first stars exploded as supernovae. But that did happen rather quickly, since the first stars were very luminous, and consequently had very brief lives.

As noted, we aren't very sure about when this first generation of stars appeared, because we can't yet observe them directly. But we do have some evidence concerning the epoch of reionization, and hence we have some idea of when it ended.

One kind of evidence involves studying the spectra of some of the most distant objects we are currently able to observe – quasars. We have detected a number of quasars at redshifts between 6 and 7. This range represents a time period from about 780 to 950 million years after the big bang.

There are absorption lines in the spectra of these quasars, and they tell us not only about the redshift, but give other information as well. Among the most important lines are those due to hydrogen that's not fully ionized, such as lines of the Lyman series. For the most part these lines are due to hydrogen in the vicinity of the source, in which case the lines are quite sharp and distinct.

But suppose there is a substantial amount of incompletely ionized hydrogen between us and the source. If this gas is at a distance sufficiently less (in terms of redshift), the absorption lines will be fuzzy instead of sharp. This effect is called a Gunn-Peterson trough.

In 2001 a quasar was identified at z=6.28, which showed a Gunn-Peterson trough, while other quasars with z≤6 did not. This suggests that reionization was mostly complete by 950 million years after the big bang, but not by 900 million years. [1][2]

Quasars, by themselves, are a possible contributor to reionization, in addition to the earliest stars. Quasars certainly produce enough high-energy photons. However, the question is whether there were enough quasars in existence during the epoch of reionization to account for the effect. Since only the very brightest quasars can currently be observed at that distance (z≥6), it's not possible to reliably estimate how many quasars altogether were around then. Rough estimates suggest there weren't enough.

There is another source of evidence for reionization, one very different from the Gunn-Peterson trough. This involves a very detailed study of anisotropies (irregularities at small angular scales) in the CMB. The CMB has many anisotropies due to conditions existing from the earliest moments after the big bang. However, if reionization occurred, certain kinds of additional characteristic anisotropies will also be present. These result from polarization of CMB light due to Thomson scattering of photons by free electrons (if such exist in sufficient numbers). Since free electrons are a by-product of reionization, they provide a very good marker, if they can be detected.

Unfortunately, the earliest data analysis (in 2003) from the Wilkinson Microwave Anisotropy Probe suggested that reionization occurred in the range 11<z<30, which corresponds to a mere 100 million to 420 million years after the big bang. This is not compatible with the quasar evidence. It's also rather implausible at the high z end, if reionization was caused by the first stars.

Fortunately, however, later data analysis (released in 2008) restated the range for reionization to 7≤z≤11. [3] z=7 still doesn't quite mesh with the quasar data, but it's pretty close. z=11 corresponds to 420 million years after the big bang, which is quite plausible for appearance of the first stars. Note that if this range is correct, then the reionization process took a lot of time, maybe 400 to 500 million years. First generation stars almost certainly weren't around that long. Such stars have very short lifetimes, and new stars of this kind can't form, because the gas from which they could form would contain considerable amounts of elements heavier than helium, precluding the formation of more stars like those of the first generation.

A third possible source of evidence comes from surveys looking for very faint, high-redshift galaxies (not quasars). Some objects have been found up to z=7.5 – about 710 million years after the big bang. [4] What isn't clear is whether these objects were either abundant enough or had hot enough stars to contribute significantly to reionization. But when the James Webb Space Telescope goes to work, sometime after mid-2013, we should be able to find many more early galaxies. The planned upgrade to the Hubble Space Telescope this year would also help – if it occurs.

Further reading:

[1] Evidence for Reionization at z ~ 6: Detection of a Gunn-Peterson Trough in a z = 6.28 Quasar – 2001 research article on first evidence for reionization (open access)

[2] First Light: Astronomers Use Distant Quasar To Probe Cosmic "Dark Age," Universe Origins (8/8/01) – press release describing the preceding research

[3] A New Day in Precision Cosmology (3/11/08) – news article describing analysis of WMAP data, including information on reionization

[4] Largest Sample Of Very Distant Galaxies Ever Seen Provide New Insights Into Early Universe (7/24/08) – press release

Tags: cosmology, cosmic dark ages

Wordless Wednesday: St. Patrick's Day

Clover grass

And don't forget that today is International Polar Day celebrating Polar Oceans.

Here are some links to some stories from the National Science Foundation about the polar regions.

* Climate-related Changes on the Antarctic Peninsula Being Driven from the Top and the Bottom of the Ecosystem

* Arctic and Antarctic-themed Activities to Bring a Breath of Polar Air to Baltimore

Propagandists and marketers agree: emotions may be more reliable when making choices

Here's yet another "study" that purports to show "gut reactions" are "better" than logical analysis in decision making. (Recent discussions of this are here, here, here.)

It's about how sales and marketing people and propagandists have learned to take advantage of your emotions for their own benefit.

Of course, that's not how it's presented....

Note the bait-and-switch technique going on in the research report: "reliability" is what the study seems to promise, but the fine print says that what you actually get is consistency.

Admittedly, "reliability" and "consistency" are nearly synonymous in terms of outcomes that marketing people want. But they may not be synonymous at all in terms of what decision-makers (i. e. you) want.

Trust Your Heart: Emotions May Be More Reliable When Making Choices (2/23/09)

"We investigated the following question: To what extent does relying on one's feelings versus deliberative thinking affect the consistency of one's preferences?" write the authors. To get at the question, the authors designed experiments where participants studied and chose among 8-10 products, sometimes relying upon their emotional reactions and sometimes calling upon cognitive skills. Their conclusion: "Emotional processing leads to greater preference consistency than cognitive processing."

Beware of marketing people who presume to advise you about, well, almost anything. But especially about either research conclusions or products they want to sell you.

Note the basic – and rather flagrantly expressed – dishonesty.

On one hand, the objective summary that the researchers offer of their study is: "Emotional processing leads to greater preference consistency than cognitive processing." In other words, the benefit attributed to reliance on emotion for decision making is consistency.

This isn't all that surprising: when people just go with their "gut feelings", the result is more likely to be the same each time the same decision is presented than if the actual specifics of the situation, which may vary from case to case, are analyzed.

This is also the outcome that marketers naturally prefer: predictable, consistent responses to marketing pitches.

But on the other hand, and this is the dishonest part, the authors also write "Indeed, our results suggest that the heart can very well serve as a more reliable compass to greater long-term happiness than pure reason."

This is a specious claim: where in their study did the researchers actually measure the happiness that experimental subjects experience as a result of their choices, as opposed to the consistency of the choices?

In other words, the unspoken idea they're pushing is actually this: you will enjoy more happiness if you allow your decisions to be determined according to how marketing has manipulated your emotions. (E. g.: Just go ask your doc for that Viagra prescription and have more fun in bed! And don't worry about whether your real problem in bed is something Viagra doesn't fix.)

If you think there may be some logic to that, just ask yourself whether letting yourself be manipulated by the greed of others is a good path to your happiness.

The sad truth of human behavior, despite illusions that humans are "rational" creatures, is that emotions are quite often much stronger motivators than reason. And they are generally a lot easier to control and manipulate than rational thinking about facts and logic.

As a result of that, people who stand to profit or otherwise benefit from the actions or beliefs they are able to persuade others to embrace have made a concerted effort, first of all, to persuade people that decisions are best made on an emotional basis.

What's their alternative, if facts and logic do not support whatever such people are advocating? They can always simply lie or engage in misdirection, and that's often done too, of course. But lies can occasionally be exposed, and in extreme cases can even be subject to prosecution (for fraud).

Think I'm making all this up? I suggest reading about one of the masters of propaganda techniques in the 20th century: Edward Bernays. He was a nephew of Sigmund Freud, and literally wrote the book: Propaganda.

Here's how that book begins:

The conscious and intelligent manipulation of the organized habits and opinions of the masses is an important element in democratic society. Those who manipulate this unseen mechanism of society constitute an invisible government which is the true ruling power of our country… We are governed, our minds molded, our tastes formed, our ideas suggested, largely by men we have never heard of. This is a logical result of the way in which our democratic society is organized…

I'll try to summarize some of the history and thinking of Bernays when time permits, but here are some things to read for now, if you're interested:

Stunt Man – book review of a biography on Bernays

Karl Rove & the Spectre of Freud’s Nephew – an essay on Bernays by Stephen Bender

Tags: marketing, propaganda

Into the Eye of the Helix

Into the Eye of the Helix

The Helix Nebula, NGC 7293, lies about 700 light-years away in the constellation of Aquarius (the Water Bearer). It is one of the closest and most spectacular examples of a planetary nebula. These exotic objects have nothing to do with planets, but are the final blooming of Sun-like stars before their retirement as white dwarfs. Shells of gas are blown off from a star’s surface, often in intricate and beautiful patterns, and shine under the harsh ultraviolet radiation from the faint, but very hot, central star. The main ring of the Helix Nebula is about two light-years across or half the distance between the Sun and its closest stellar neighbour.

NGC 7293 – click for 1280×1185 image

More: here

Book Review: Polar Worlds

This month marks the end of a two year journey of exploration, discovery, wonder, and advocacy. March 31st marks the end of International Polar Year (IPY) 2007-2009.

In fact, Wednesday, March 18, 2009 is International Polar Day celebrating Polar Oceans. The ocean or marine ecosystem is a very important part of the polar biome. The animals of the polar regions - both the north and south poles - depend on a variety of seafood species for nutrition - such as krill, fish, ocean birds, and ocean mammals. The polar food webs are complex and interesting. And a perfect text for IPY and International Polar Day - Polar Ocean is this book.

Title: Polar Worlds - Life at the ends of the earth
Author & Illustrator: Robert Bateman
Publisher: Scholastic/Madison Press

I became a fan of Robert Bateman when I read his book Birds of Prey. He is a very talented artist. All of this sketches and painting of the Arctic and Antarctic animals look very life-like, more like photographs than paintings. The book gives a very thorough introduction to all of the types of animals that call the Arctic and Antarctic home. Though both of these polar regions are cold and remote, they are very different from one another.

The Arctic region has been inhabited by people for many thousands of years. The people of these many northern nations have had to survive the cold and depend on animals such as the polar bear, caribou, sheep, whale, and water birds for food, clothing, and fuel.

The Antarctic hasn't had permanent human settlements, but human impact has been strong for a few hundred years. Sailing and whaling were once very important industries in the southern polar regions. But thanks to protective laws the oceans of the Antarctic region are now protective and refuge area for sea animals, especially whales. Bateman introduces readers to the many bird and seal species that call the South pole and its waters home.

What I especially like about Bateman's artistry is his ability to accurate portray animal anatomy. With his pen and colors he captures the shape and movement of animals very well. I also enjoy his very-easy to read text. This book is intended for young reader, intermediate school grades, he can also maintain the attention of adults, too. It's a great science book for your school or home library.

Plus, as I mentioned during Week of the Blue, marine habitats and animals are in serious jeopardy. I enjoy learning about nature and animals and I love sharing what I learn with you. I hope I also inspire in you a desire to make our world a better ecosystem for all - humans and wildlife. I hope you join with me to help protect the endangered polar bear. Encourage the United States Secretary of the Interior, (the government department responsible for protecting our common heritage resources) -Ken Salazar to put into effect regulations to provide the polar bear the legal protections it needs to survive. This is a perfect community service activity for celebrating International Polar Day - Polar Oceans. After all, polar bears depend on the polar oceans for survival.

Click here to find out more and sign the petition.

Thank you.

MicroRNA and cancer II

We haven't recently discussed the role of microRNA in cancer. Last time (February 2008) is here. There have been some relatively recent research announcements, so let's have a look.

If you want a refresher on the subject, here's a good introductory overview from Cancer Research UK: Micro RNAs and cancer. Although this piece is fairly elementary, it does have many good links to actual research papers.

Now let's jump into a few summaries of recent research.

What's Feeding Cancer Cells? (2/17/09): Cancer cells grow and multiply rapidly, so they need lots of nutrients. Much is already known about how cancer cells use blood sugar, but other nutrients are also needed. One of these is the amino acid glutamine. This research found that the transcription factor Myc is able to enhance the expression of the enzyme glutaminase (GLS) in cellular mitochondria. GLS is the first enzyme that processes glutamine to produce energy in mitochondria. (Overexpression of Myc is frequently found in cancer – see here.)

The research found that depriving cancer cells of GLS slowed their growth significantly. It was suspected that Myc could directly up-regulate the GLS gene, but it was not that simple. Instead, it appears that Myc down-regulates genes for two types of microRNA: mi-R23a and mi-R23b. Since these mircoRNAs interfere with the GLS messenger RNA, the net effect of Myc is to enhance GLS production.

Research abstract: c-Myc suppression of miR-23a/b enhances mitochondrial glutaminase expression and glutamine metabolism
A new discovered mutation can hold the key to treat a large number of different cancers (2/17/09): Since microRNA normally inhibits production of certain proteins, if the proteins affected promote cancer, the inhibitory miRNA will counteract this. This research examined cells of twelve different cancer types.

The basic finding was that mutations of the gene TARBP2 disrupts a pathway that produces anti-oncogenic microRNAs. Mutated TARBP2 diminishes TRBP protein expression, resulting in a defect in the processing of miRNAs. Specifically, the DICER1 protein, which is necessary for miRNA production, is adversely affected.

Research abstract: A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function
Micro RNA Plays A Key Role In Melanoma Metastasis (2/15/09): Metastasis is the main process by which cancer becomes deadly, and it is especially problematic in melanoma. In order for cancer cells to metastasize (spread to another body location) they must become able to migrate and establish themselves in the new location. This research finds that the microRNA miR-182 assists in this process.

MiR-182 is frequently up-regulated in human melanoma, usually because melanoma cellular DNA contains extra copies of the miR-182 gene. This up-regulation was shown to assist metastasis. Conversely, down-regulation impedes invasion and triggers apoptosis. Over-expressed miR-182 is shown to repress the expression of two tumor suppressors, FOXO3 and MITF, which are both transcription factors. (For more on FOXO3, see here.)

Research abstract: Aberrant miR-182 expression promotes melanoma metastasis by repressing FOXO3 and microphthalmia-associated transcription factor
New Genes Involved In Acute Lymphoblastic Leukemia Play Fundamental Role In Prognosis Of The Disease (2/6/09): This investigation found that 13 microRNAs were epigenetically regulated in an abnormal way in many patients with acute lymphoblastic leukaemia (ALL). This means that instead of having actual gene mutations, certain parts of the DNA were methylated in an unusual way, so that the underlying genes, which coded for microRNAs, were down-regulated. More precisely, certain histones of the cell's chromatin were methylated, so that genes located on the DNA wrapped around those histones would not be expressed. The genes involved coded for microRNAs that, evidently, are important for suppressing cancer. When approriate steps were taken to reverse abnormal epigenetic regulation of the affected genes, expression levels rose, confirming that the abnormal methylation patterns were responsible for down-regulation.

65% of 352 ALL patients had one or more methylation abnormalities affecting microRNA under investigation. There was a highly significant positive correlation between patient survival at 14 years after diagnosis and absence of such abnormalities. Consequently, tests for methylation problems with the appropriate microRNA genes should be good predictors of survival prospects.

Research abstract: Epigenetic regulation of microRNAs in acute lymphoblastic leukemia
Researchers Identify Another Potential Biomarker For Lung Cancer (1/13/09): The research showed that smoking impacts bronchial airway gene expression. Various miRNAs were found that were differently expressed in bronchial airway epithelial cells, mostly down-regulated. Messenger RNAs were also identified, whose expression was inversely correlated to the miRNA expression (so that the corresponding genes appear to be down-regulated by the miRNA.)

MiR-218 was especially noteworthy. It is known to be strongly affected by smoking. The conclusion is that miR-218 levels modulate airway epithelial gene expression response to cigarette smoke, suggesting a role for miRNAs in regulating response to environmental toxins.

Research abstract: MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium
Molecule Linked To Muscle Maturation, Muscle Cancer (12/31/08): The study clarified the role of MiR-29 in myogenesis (muscle cell formation) and found that its down-regulation is associated with rhabdomyosarcoma (RMS), a cancer caused by the proliferation of immature muscle cells. While miR-29 is required for maturation of myoblasts (immature muscle cells), it is also found to be mostly absent from RMS cells.

The study found, further, that the transcription factor NF-κB is responsible for down-regulating miR-29. (NF-κB is an old friend of ours. See here for a small part of the story about its role in inflammation. There's also much more to be said about the role of NF-κB in cancer, where it provides an important connection between inflammation and cancer.)

NF-κB acts to repress miR-29 through another transcription factor, YY1, and Polycomb-group proteins (which remodel chromatin to block transcription factors from DNA promoter sequences).

During myogenesis, NK-κB and YY1 are down-regulated, permitting expression of miR-29, which then further down-regulates YY1 and accelerates cell differentiation. However, in RMS the NF-κB–YY1 pathway remains active, silencing miR-29 and inhibiting differentiation. But reconstitution of miR-29 in RMS in mice inhibits tumor growth and stimulates differentiation,

Research abstract: NF-κB–YY1–miR-29 Regulatory Circuitry in Skeletal Myogenesis and Rhabdomyosarcoma
Harnessing MiRNA Natural Gene Repressors For Anticancer Therapy (12/1/08): This research investigates the potential therapeutic use of miR-181a through its ability to repress expression of selected genes. If successful, this would provide a very clever kind of immunotherapy for cancer and possibly other diseases.

In immune system T cells miR-181a is highly expressed in developing T cells, but is markedly down-regulated in mature T cells. Mouse bone marrow cells were engineered to express desired therapeutic genes only when miR-181a is down-regulated. These cells were transplanted into mice and allowed to develop into mature T cells. The proteins repressed by miR-181a would therefore not be found in the immature cells, but would show up in the mature T cells. And so when the genes repressed by miR-181a corresponded to proteins that direct T cells to attack tumor cells expressing the protein hCD19, mice with the engineered bone marrow cells were able to reject tumors expressing hCD19.

Research article (open access): Harnessing endogenous miR-181a to segregate transgenic antigen receptor expression in developing versus post-thymic T cells in murine hematopoietic chimeras
Molecule Linked To Aggressive Cancer Growth And Spread Identified (11/13/08): EZH2 is a polycomb group protein, which helps maintain transcriptional repression of genes over successive cell generations. It contributes to the epigenetic silencing of target genes and enables the survival and metastasis of cancer. The research indicates that miR-101 inhibits the expression and function of EZH2 in cancer cells.

The researchers found that miR-101 is significantly underexpressed in a variety of cancers, including prostate and breast cancer. In human prostate tumors miR-101 expression decreases as cancer progresses and expression of EZH2 increases. MiR-101 is coded for at two locations in cell DNA. One or both of those locations is found to be defective in 37.5% of localized prostate cancer cells and in 66.7% of metastatic cells. This suggests that that underexpression of miR-101 is responsible for overexpression of EZH2 and consequent cancer progression.

More: here (11/13/08)

Research abstract: Genomic Loss of microRNA-101 Leads to Overexpression of Histone Methyltransferase EZH2 in Cancer

Further reading:

MicroRNA—implications for cancer – excellent open access review article

Tags: cancer, microRNA

Beware the Ides of March - Keep your eyes open

Keep your eyes open for what?
For all of the nature that is beginning to emerge, sprout and bloom because spring is near.

Phenology is the study of timing of natural events. I'm always encouraging you to go outside and observe nature, now I'm also asking you to jot down notes of your observations (if you don't already).

Science and nature watching organizations depend on great nature-loving watchers like you to keep their data bases up-to-date. Plus, your observations help scientists determine if there may be some changes in plant and animal winter and spring transitions changes due to climate change. Remember, nothing we know about the natural world in science comes to our knowledge without lots of information to support the idea (hypothesis). So open your eyes and report your results.

The Museum of Science (Boston, Massachusetts) celebrates a second year of Firefly Watching. April 11 is Firefly Day.

Join the Firefly Watch Brigade. Observe fireflies in your hometown and report your observations to the Museum of Science database.

image credit: http://www.cirrusimage.com/beetle_firefly_Photuris_lucicrescens.htm

The National Phenology Network is an online community of scientists and citizen scientists. Join as we all catalogue our plant observations. Hat tip to Kim Hannula.

Photo by Alecia Hoyt

And please leave me a comment and let me know what you're seeing (and when) in your backyard. Keep having Urban Science Adventures! ©

***Update: Later today, 4:30 pm. Look what I noticed blooming in my frontyard.***

Plus other signs of bloom.

Week of the Blue: What's next for the Blue Whale?

The show airs again Sunday, March 15, 2009. But what happens next? What can we do to help the Blue whale and the very much threaten marine ecosystem. Can there be a balance between human needs and nature? Must we always be in conflict?

image credit: http://s79.photobucket.com/albums/j129/Volcanoes9/WHALES/?action=view&current=BlueWhale.jpg

For example, how does import and export of goods across the ocean impact wildlife. As the show detailed, it does, but we're not sure of exactly how deep the impact is. The special also introduced many of us to cultures that consume whale meat. How does the consumption of seafood products - including fish and shrimp impact marine ecosystems.

I hope it is becoming apparent to you that everything in this world is connected. Nothing we do is without consequences. As ecologists often say, there are downstream effects. I do know that nothing positive happens with out knowledge. The television special was just the first step in learning more. The next move is ours.

I've put together a list of web resources to help you in your research.Many of these links come from the books I recommended to you earlier this week. (Great books,huh?)

American Cetacean Society www.acsonline.org/factpack

Interspecies.com - hear sounds of beluga whales www.interspecies.com/pages/belgua%20sound.html

Save the Whales http://www.savethewhales.org/

Whale Net http://www.whale.wheelock.edu/

Whale Watch www.whalewatch.com/research/behaviors/php

NOAA Fisheries Kids Pages www.nmfs.noaa.gov/pr/education/whales.htm

National Geographic Animal Pages http://www.animals.nationalgeographic.com/

Cornell University Macaulay Library of Animal Sounds - Marine Collection http://www.birds.cornell.edu/MacaulayLibrary/explore/marine

Ocean Research and Conservation Association www.oceanrecon.org/research.htm

Finally, Cathy Preston, a graduate student in marine conservation at the University of California San Diego interested in Marine Policy and Conservation. Part of her research project is about sustainable seafood practices. Sustainable seafood practices might be one of the ways to balance human and nature conflicts. Her research involves asking people about their seafood consumption and choices. She has an online survey that you can fill out and only takes a few minutes. As a fellow graduate student and scientist, I know how hard it can be to get enough data. I am asking all you, my very lovely readers to participate. Here is the link to the survey.

Thank you very much.

Week of the Blue: Feeding at Sea

In the Kingdom of the Blue Whale, the researchers came across a dead blue whale while at sea. The tell-tale signs of death were all-around. The floating bloating body of the dead whale. The circling and squawking scavengers from the sky - in this case sea gulls. Finally, the feeding frenzy of blue sharks in the ocean. Death is never a pleasant sight or smell in any natural environment; however it is a part of the life cycle and the food cycle.

Dead animals provide a valuable bulk source of nutrition to the remaining animals in the food web. Meat is a very valuable source of protein, on which the sea gulls and sharks were partaking. And had the whale sank to the ocean floor, which normally happens, a frenzy of other animals would have had the opportunity to feast as well. Though the death and location of a whale is completely random, in fact there are thousands of organisms large, small, and microscopic who greatly depend on them.

However, the dead whale from the special washed up on shore. In fact, the special showed another blue whale that had washed up on shore after death. Though sea gulls and other land animals willing and capable of feasting on the whale, it won't be handled nearly as efficiently as it would have been had the carcass remained out at sea. When a dead whale washes to shore, usually people have a hard time dealing with the sight and especially smell of the decomposing animal. In urban areas this is a big problem. As a result, teams of people come to assist. Though it was sad to see the dead baby whale (which had been born to soon from the shock of its mom's death), scientists now know more about fetal and baby blue whales.

This is a great opportunity for researchers to collect samples or learn more about whale anatomy. For example the researcher interested in whale hearing behavior was able to collect an intact whale ear bone structure. Her research in whale ear anatomy may prove beneficial in helping us understand how whales make and receive sounds - from each other and the huge shipping vessels that cause whale death.

Wordless Wednesday: Blue Oceans, Blue Skies

It's Wordless Wednesday, Week of the Blue style, so it's also a Watery Wednesday.

I'm still celebrating all things marine and including a little urban marine ecology, too.

These pictures are from my trip to Florianopolis, Brazil to the International Ethological Conference (IEC) in 2003.

This is an aerial shot of Miami, Florida (USA). As one of the nation's largest cities, this coastal city is a typical urban marine ecosystem.

Florianopolis is actually an island, surrounded by beaches of the Atlantic Ocean.

A view from the center of the moderately populated town, the ocean is in the background.

Can you see it?A better view of the ocean.

I stayed in a lovely little pousada, appropriately named, Villa of the Water (translated).

This is the view from my door at the pousada. The ocean was literally only 2 blocks away.

The very cold waves crashes. It was August, and that is winter time in the Southern Hemisphere.

The island is connected to other half of Florianopolis and mainland Brazil via the Hercilio Luiz Bridge planned by Gustave Eiffel, yes, the same man who designed the Eiffel Tower in Paris (which I hope to visit at my next IEC Conference later this year).

A view of the mainland metropolis city of Florianopolis.

The Kingdom of the Blue Whale

I watched the show with excitement and anticipation, both nights. But each time a close-up of a blue whale was on the screen, I tilted my head in an effort to comprehend the position and orientation of the whale.

Am I the only who looks at the blue whale and thinks, "Is it swimming up-side down?"

But it isn't. The picture (above) is of a blue whale swimming right-side-up, belly down. The thing is I have a bit of sensory bias.

When I compare the blue whale to aquatic animals I do know, there are some differences in body features. First, the fish I am familiar with have backs that are typically rounded out and the bellies are flat.

Second, the facial features of blue whales are assembled very differently than other animals, land animals, I know. Imagine the mouth is the horizontal line that divides the face into top and bottom parts. In animals like mice, birds, and dogs, you encounter the nose, eyes and top of head, in that order.

Below the mouth are the chin and lower-jaw. The top half of the face tends to be bigger than the bottom half. I call this the top/bottom face ratio.

Like other marine mammals, the whale's nostrils (nose) is located on the top of the head. The eyes are to the side, but are still above the mouth. So, everything is still on its 'proper' side of the horizontal line but moved around. But the top/bottom face ratio is completely the opposite. Blue whales have a very large bottom half of the face. This combined with the flat back are the reasons why the blue whale look up-side down to me.

But think about it, that larger bottom jaw on the blue whale comes in handy. These guys are big eaters; they can consume approximately 8000 lbs of krill a day. They need those big, fleshy jaws to scoop up as much water an krill as they can.

I commend the producers of the show for using quality film footage and three-dimensional animated graphics to detail the life and perils of the blue whale. I certainly learned about their behavior and natural history, but it seems so did the research team. Despite being the largest animal in world, we know so little about this great creature. Even the teams of scientists are trying to put the pieces together. And that's exactly what National Geographic shows us. They give us a front row seat to the scientific process. As I sometimes tell students, science is a verb --it's what you do. Through the special, we witnessed these teams of scientists in the field and the lab doing science - the waiting, the measuring, the collecting, the stalking, the re-measuring, more waiting, observing, collecting, and observing some more. Science is laborious and many times we come back with nothing. it can be sad deflating at time.

However, it makes the success of getting data even sweeter. I was so enthralled with the progression of the story that I was as excited as the scientists were when they began to meet their research benchmarks.

1. They confirmed that these animals feed all year in the tropical oceans. This was confirmed, the way all mammalogists confirm it - they collected whale poop.

2. They observed what seemed to be very convincing signs of courtship behavior among adult whales. This would suggest that those tropical waters are also important for mating.

3. They observed a baby blue whale with its mother. Capturing this infant on film was historic. I must confess, I was disappointed to not have seen the live birth, but the 3-D animation sufficed my curiosity. Again, this provides evidence that these warm seas near Costa Rica are indeed an important habitat for the conservation of this species.

It was an awesome film and it completely met my expectations. Thanks, Nat Geo!

Week of the Blue Book Review - Whales and Oceans

I have two interesting children's science books on my shelf that are perfect for the Week of the Blue tribute to Marine & Ocean Biology.

National Geographic The Kingdom of the Blue Whale television program gave all of us land-locked regular people a chance to experience the life of marine researchers - on the sea and in the lab (or hotel room lab). Hey, scientists are clever and adaptable people. Like you, we make do with the resources we have.

So, immediately after the program, I cracked open my Ocean and Marine Wildlife Books and starting reading.

Title: Face to Face with Whales

Authors: Flip and Linda Nicklin

Publisher: National Geographic

This was truly a beautiful coincidence to have a book about whales from the same organization that brought us this television special. What I enjoyed the most was how the authors come right out and talk about whale behavior. In fact, they introduce us to two Whale Behavior Biologists - Jim Darling and Jonathan Gordon. The authors, Flip and Linda Nicklin, have spent a lot of time on whale research boats and have captured some amazing photographs of whale all kinds of whales - Narwhals, Belugas, Sperm Whales, Humpbacks, Minkes, Fin Whales, and the star of the show Blue Whales. This trade book is very easy to read and a great follow-up to the television program. Like the show, it includes references to conservation issues and concerns for all whale species and offers suggestions for how each of us can make a difference.

Title: WOW! World's of Wonder Ocean Life

Author Carolyn Franklin

Publisher: Children's Press of Scholastic

Like the previous title, this was also a great follow-up read to the television show. The book introduces younger readers to marine wildlife from the deep dark ocean to the sandy shores. I give the book thumbs up for being very inclusive - it describes and illustrates plankton, all kinds of squirmy wormy and wool invertebrates, fish - small, medium, large, and extra-large, the plant life and algae, cephalopods, corals,the reptiles birds and mammals, and the sessile organisms like barnacles, starfish and anemones. The book features factoids about ocean life and ecology, particularly food chain relationships among all of the sea creatures. It is also very colorful. I was distracted by it, but I bet the school kids will love it. The book even includes a True & False question about the Mightily Beloved Blue Whale - Does it eat up to 7,900 pounds of animal plankton a day? Tick, tock. After watching the special you should able to answer that. If not, you can cheat a little here.

Now, if you missed the show on Sunday, then don't despair. It airs again tomorrow, Tuesday, March 10, 7 pm central time on the National Geographic Channel.

Check it out!

Splitting of prime ideals in quadratic extensions of &#8474, part 1

Our discussion of algebraic number theory returns by popular demand. Way back last April we presented some generalities on factorization of prime ideals in extension fields. (For explanation of what that means, including other necessary concepts, you'll have to review earlier installments of this series, which can be found here.)

If this is all Greek to you, I apologize, but that's unavoidable at this stage of a rather technical subject. You may want to go back to the earliest parts of the series to see how the subject got its start and why it may be interesting.

The discussion in the previous installment probably seems rather dry and abstract, but when we look at simple examples, such as quadratic extensions, why it's interesting becomes clearer.

Because of how the ramification indexes and inertial degrees are related, for any prime ideal (p) of ℤ there are only three different possibilities for how the ideal factors in the ring of integers of a quadratic extension:

(p)=P₁⋅P₂, so (p) splits completely. (e=f=1, g=2)
(p)=P is a prime ideal in ℚ(√d), so p is inert. (e=g=1, f=2)
(p)=P² where P is prime, and p is ramified. (f=g=1, e=2)

It turns out that there are simple criteria for each of these cases. But figuring out what the criteria are is tricky.

Recall that in ℚ(√3) we found (13)=(4+√3)⋅(4-√3) and (-11)=(8+5√3)⋅(8-5√3), so both (11) and (13) split completely. Clearly, (3)=(√3)², so (3) is an example of a prime ideal if ℤ that is ramified. How about an example of a prime ideal that is inert in the extension? This is a little harder for a couple of reasons. (p) will be inert just in case it neither splits nor is ramified, but we don't yet have simple criteria to rule out those cases.

So let's back up a little and look at the details. We found examples where (p) splits in the integers of ℚ(√3) by solving the equation ±p=a²-3b², because that gave elements a±b√3 whose norm was ±p. Being able to find such elements guaranteed that the prime split. But ℚ(√d) with d=3 is a special case, since here d≡3 (mod 4). In that case, and also if d≡2 (mod 4), the integers of the extension have the form a+b√d with a,b∈ℤ.

If d≡1 (mod 4), integers can also have the form (a+b√d)/2, with a,b∈ℤ, and we might have a factorization like (p) = ((a+b√d)/2)⋅((a-b√d)/2), so we would have also to consider solvability of ±4p=a²-3b². If we were to look at solvability of the approriate equation, according as to whether or not d≡1 (mod 4), the solvability would be a sufficient condition for (p) to split (or ramify if a=0). Notice that this sufficient condition for (p) to split holds regardless of whether or not ℚ(√d) is a PID.

Now we need to find a convenient necessary condition for (p) to split. Unfortunately, solvability of one simple equation is not a necessary condition in general. It would be, as we'll see in a minute, if the ring of integers of ℚ(√d) happens to be a PID, as is true when d=3. However, in quadratic extensions where the ring of integers isn't a PID, being unable to solve the applicable equation doesn't guarantee (p) cannot split, because there might be non-principal ideals that are factors of (p).

So let's ignore that problem for a moment and just focus on the case where the ring of integers of ℚ(√d) is a PID. Can we then find a necessary condition on p for (p) to split or ramify, i. e. for (p) to not be a prime ideal of the integers of ℚ(√d)? That is, what must be true about p if (p) splits or ramifies?

If (p) splits or ramifies, then (p)=P₁⋅P₂ for nontrivial ideals P_i. (The ideals are the same or distinct according as (p) ramifies or splits.) Assuming ℚ(√d) is a PID, then P₁ is generated by a+b√d where both a,b∈ℤ, if d≡2 or 3 (mod 4), or else by (a+b√d)/2 with a,b∈ℤ, if d≡1 (mod 4). Likewise, the conjugate ideal P₂ is generated by a-b√d or (a-b√d)/2. Since p∈P₁⋅P₂, by definition of a product of ideals, p is of the form p = ε(a+b√d)(a-b√d) = ε(a²-db²) or p = ε(a+b√d)(a-b√d)/4 = ε(a²-db²)/4 for some integer ε of ℚ(√d).

Recall that the norm of an element of a Galois extension field is the product of all conjugates of the element. So for an element that is also in the base field, the norm (with respect to a quadratic extension, which is always Galois) is the square of the element. Taking norms of both sides of the possible equations, then either p² = N(&epsilon)(a²-db²)² or 16p² = N(&epsilon)(a²-db²)². For simplicity, consider just the first case. Then N(ε) is a positive integer that has to be 1, p, or p². If N(ε)≠1 then N(a±b√d) = a²-db² must be ±1, so a±b√d must be a unit, and both P_i must be non-proper ideals (i. e. equal to the whole ring). Hence N(ε)=1. This will be true also in the other case (when d≡1 (mod 4)), so ±p=a²-db² or ±4p=a²-db². Consequently, solvability of the appropriate equation (depending on d mod 4), is a necessary condition for (p) to split or ramify.

So we have a necessary and sufficient condition for (p) to split or ramify in ℚ(√d), in terms of solvability of Diophantine equations, provided O_ℚ(√d) is a PID. Since the only other possibility is for (p) to be inert, we also have a necessary and sufficient condition for that.

However, still assuming that O_ℚ(√d) is a PID, we can find a further necessary condition for (p) to split or ramify. Take those equations we just found and reduce them modulo p. Then both equations become a²≡db² (mod p). Since p is prime, ℤ/pℤ is a field. Assume first that b≢0 (mod p). Then b has an inverse in the finite field. So we have d≡(a/b)² (mod p). In other words, d is a square mod p. This is the additional necessary condition we were looking for on p in order for (p) to split or ramify. Since it's a necessary condition, if d is not a square mod p, then (p) must not split or ramify, and thus p is inert. And so, for d to be a non-square mod p is a sufficient condition for p to be inert.

(What if b≡0 (mod p)? Then b=b₁p. So ±p = a² - (b₁p)²d or else ±4p = a² - (b₁p)²d. Either way, p∣a, hence p² divides the right side of either equation, and hence the left side also. But that's not possible unless p=2 – which is always a special case.)

To summarize, then, let p≠2 be prime and d square-free and not 0 or 1. Then the solvability of ±tp=a²-db² (where t is 4 or 1 according as d≡1 (mod 4) or not), is sufficient for (p) to split or ramify. And if the integers of ℚ(√d) are a PID, then solvability of the appropriate equation provides a necessary and sufficient condition for (p) to split or ramify. Further, in that case, d being a square mod p is necessary for (p) to split or ramify.

Remarkably, d being a square mod p is a necessary and sufficient condition for (p) to split or ramify, even if the integers of ℚ(√d) aren't a PID, but that's harder to prove. Since solvability of Diophantine equations is generally not obvious by inspection, it's very convenient to have a necessary and sufficient conditions for (p) to split or ramify simply in terms of the properties of d mod p.

In the next installment, which hopefully will not be as long in coming as this one, we'll show a much cleaner way to state necessary and sufficient conditions for (p) to split, ramify, or remain inert, in the case of any quadratic extension of ℚ, whether or not the ring of integers is a PID. This will be done in terms of what has long been called a "reciprocity law".

However, that will be only the beginning. It turns out that there are far more general kinds of reciprocity laws for many other types of field extensions. That's what "class field theory" is all about, and why the whole subject is so appealing, once you get the basic ideas.

Tags: algebraic number theory

Subscribe to: Posts (Atom)