Human stem cell brain injection approved by FDA

The FDA has approved a procedure to be done at Stanford University involving stem cells. The stem cells are harvested by a private group from aborted fetuses. "Immature neural cells" (brain stem cells) are yoinked out of the dead not-quite-humans and injected into the brains of children sufferring from Batten disease.

Batten disease is caused by a defective gene that fails to create an enzyme needed in the brain to help dispose of brain cellular waste. The waste piles up and kills healthy cells until the patient dies. Most victims die before they reach their teens.

The kids being experimented on WILL DIE within years without the experiment. They'll probably die anyway, but maybe more slowly. The injected neurons take over the kid's brain and make it work right.

Astrology and ID both scientific, claims Pennsylvania prof

A trial facing the US courts is over whether K-12 teachers in Dover, PA, should read a statement to their students questioning Darwinian evolution before teaching the content. Eleven parents are sueing the school board saying that the statment is tantamount to promoting religious creationism, while the school board claims that they are only making the students aware of the controversy in an unestablished claim. In the quote below, Rothschild is the attourney for the plaintiffs (the 11 pro-evolution parents), while Behe is a witness for the defense (pro-intelligent design school board). Behe is a biochem prof at University, Bethlehem, PA.

Rothschild told the court that the US National Academy of Sciences supplies a definition for what constitutes a scientific theory: “Theory: In science, a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, inferences, and tested hypotheses.”

Because ID has been rejected by virtually every scientist and science organisation, and has never once passed the muster of a peer-reviewed journal paper, Behe admitted that the controversial theory would not be included in the NAS definition. “I can’t point to an external community that would agree that this was well substantiated,” he said.

Behe said he had come up with his own “broader” definition of a theory, claiming that this more accurately describes the way theories are actually used by scientists. “The word is used a lot more loosely than the NAS defined it,” he says.

Hypothesis or theory?

Rothschild suggested that Behe’s definition was so loose that astrology would come under this definition as well. He also pointed out that Behe’s definition of theory was almost identical to the NAS’s definition of a hypothesis. Behe agreed with both assertions.

The exchange prompted laughter from the court, which was packed with local members of the public and the school board.

Behe maintains that ID is science: “Under my definition, scientific theory is a proposed explanation which points to physical data and logical inferences.”

“You've got to admire the guy. It’s Daniel in the lion’s den,” says Robert Slade, a local retiree who has been attending the trial because he is interested in science. "But I can’t believe he teaches a college biology class."

What's wrong with Astrology

Have you noticed that when you click on people's blogger profiles, it lists their astrological sign?

There are numerous things wrong with astrology.

•At its vaguest, it is unfalsifiable by making general statements that can apply to anyone. (I.e., this aspect is unfalsifiable.)

•At its most precise, it should have been able to predict the discovery of planets such as Neptune, Uranus, Pluto, and maybe even asteroids (Ceres) and Kuiper Belt Objects (Quaoar, Sedna, Xena/2003UB13). Astrologers failed to do so, and therefore have failed the one objective test that we could administer. (I.e., this aspect has been falsified.)

•Precession - a wobbling effect of the Earth's axis - means that you weren't actually born in your birth sign, but the one after. The "first point in Aries" (vernal equinox, first day of Spring) actually is in Pisces, and it's nearly the "Age of Aquarius."

•They left out Ophiuchus. There's actually 13 zodiacal constellations, and it's the extra.

Now that you've listened to me rant about it, listen to someone else rant, and then try very hard not to mock ID proponents.

Brits asked to count frogs for science

Worldwide one-third of frog species are facing extinction from two diseases, one viral and one fungal. This is of course in addition to their sensitivity to pollution, climate change, and destruction of its natural habitat. If you live in Britain, you can help with the effort to track frogs and determine whether they're sick by visting the website Froglife and filling out and mailing a 14-question survey. Not that bad a task to help protect frogs worldwide. One thousand responses are needed to adequately sample British frogs.

HST repair?

This one's a request for info if any of you know, rather than an explanation.

Formerly, NASA had said the minimum number of shuttle flights needed to construct the orbiting station was 28; now, that number has been reduced to 18, plus another flight to repair the aging Hubble Space Telescope.

Has anyone heard anything, or is this a typo or new thing? The AAS (American Astromical Society) doesn't say anything, and if anyone would know, they would.

Biological basis for lying

A USC study has found the first proof of structural brain abnormalities in people who habitually lie, cheat and manipulate others.
...
The subjects were taken from a sample of 108 volunteers pulled from Los Angeles’ temporary employment pool. A series of psychological tests and interviews placed 12 in the category of people who had a history of repeated lying (11 men, one woman); 16 who exhibited signs of antisocial personality disorder but not pathological lying (15 men, one woman); and 21 who were normal controls (15 men, six women).
...
After they were categorized, the researchers used Magnetic Resonance Imaging to explore structural brain differences between the groups. The liars had significantly more “white matter” and slightly less “gray matter” than those they were measured against, Raine said.
...
[Yaling] Yang, the study’s lead author, said the findings eventually could be used in making clinical diagnoses and may have applications in the criminal justice system and the business world.

“If [the findings] can be replicated and extended, they may have long-term implications in a number of areas,” said Yang, a doctoral student in the USC department of psychology’s brain and cognitive science program.

“For example, in the legal system they could potentially be used to help police work out which suspects are lying. In terms of clinical practice, they could help clinicians diagnose who is malingering – making up disability for financial gain.

“And also in business, they could assist in pre-employment screening, working out which individuals may not be suitable for hiring.

Controversy in Human Evolution

This one really IS a controversy. On the Indonesian island Flores, inside a cave, bones from a number of humans from some 12,000 to 95,000 years ago have been found. "Human" here is a broad term including neanderthals down to modern homo sapiens sapiens. These particular bones are significantly smaller than those of other homo sapiens of the same time, and most archaeologists/biologists believe they're of a new species and call them homo floriensis, familiarly known as Hobbits. A number of scientists remain unconvinced; they point out that these could've been an isolated group of dwarf homo sapiens. Only time will tell which hypothesis will win out and become the accepted theory.

Untestable Hypothesis and Falsifiability

The Scientific Method has some five key steps to it, as mentioned previously, and reminded here.

1.Observation/Question

2.Hypothesis

3.Prediction

4.Experiment

5.Conclusion

One of the toughest parts of the Scientific Method is simply determining whether it's possible to design an experiment to test your hypothesis. If it IS possible to test it, and there are clear conditions for what counts as refuting your hypothesis, the hypothesis is called falsifiable, and this is a good thing in science. "Falsifiable" means the same thing as "testable," it doesn't mean "proven false." Yeah, it's confusing. So some examples may help.

Hypothesis: There are NO black swans.
Test: Look for a black swan.
Falsifiable? Yes
Potential Falsification: Finding a black swan.
Truth Status: False (there are black swans).

Hypothesis: There are pink elephants.
Test: Look for a pink elephant.
Falsifiable? No
Potential Falsification: None. If you looked around the whole world, maybe it was hiding in Japan while you were in New Zealand. If you saw the whole world simultaneously, maybe it's on Mars. Or another solar system. It's impossible to actually carry out the test.
Truth Status: So far it appears false, but we're not sure. The statment "there is no such thing as a pink elephant" is a good example of something that a non-scientist would call a fact but scientists would say is unproven.

Hypothesis: Throwing a virgin in an active volcano appeases the gods and prevents the volcano from erupting.
Test: Don't throw a virgin in volcanos.
Falsifiable? Partially.
Potential Falsification: The problem is that if you do throw in the virgins and it doesn't erupt, you're not sure if it's that or something else which prevented the volcano from erupting. If you don't throw in virgins and it does erupt, you're not sure if it's that or something else which did make it erupt. The only condition which definitely would falsify it would be if we threw in a virgin and the volcano erupted anyway. Another way to think about it is that we can't test supernatural forces.
Truth Status: Essentially false, as we've got other explanations for volcano eruption that do not evoke supernatural forces.

Hypothesis: Waging war in Iraq keeps America safe.
Test: Don't wage war in Iraq and see if we get "less safe."
Falsifiable? Perhaps, but are we willing to try the test? And how would we quantify it?

Responding to the president's [Oct 6 (?), 2005] address , the Senate Minority Whip, Dick Durbin, D- Illinois, said the speech left too many questions about the Iraq war unanswered.

"He owes it to the American people -- and the Democrats are calling on him to tell the American people -- how will this end? How can we measure success? How can we get beyond the generalities of the speech that we heard today?" Durbin said.

NASA's Chewbacca

Today I heard of a logical fallacy that Wikipedia refers to as the Chewbacca Defense, as per a South Park reference. This is an argument that attempts to convince by confusion, see also the red herring fallacy.

The example that prompted me to blog about it is that NASA has been accused of misspending money by using its own planes to fly its employees around the country, rather than buying cheaper airline tickets. Said Sen. Susan Collins, R-Maine,

"In the environment we're in right now with tight federal budgets and the demands of responding to Hurricane Katrina, it is particularly disturbing to learn that a federal agency is not being a more careful steward of the taxpayers' dollars. There's also a waste of fuel here, too."

Um, someone explain to her that while everyone's sad about Katrinia, and yeah gas prices suck, it doesn't make NASA any more guilty of things they've done for the past 15 years. Next thing you know, in addition to reductio ad Hitlerum and reductio ad terrorism arguments being common, you'll have reductio ad Katrina arguments.

Virus and Bacteria Evolution

The clearest and most current example of evolution that I can think of is the modern-day mutation of viral and bacterial strains. Antibacterial resistant strains of bacteria are cropping up in hospitals across the industrialized world, where we overuse antibacterial washes and such. The chemicals kill most of the bacteria on your hands, but a few hardy ones manage to survive. They pass on their hardy traits to make a new population of hardier (resistant) bacteria.

The avian flu (H5N1) rampant in Asia is another example. On the one hand, some strains of it are mutating to become resistant, which means they will come to dominate their weaker peers. And on the other hand authorities worry that a strain transmissible from human to human will develop. This would be devastating to humankind, as 150 million could die (around 2.3% of the 6.5 billion in the world), and of course it'd start with third world countries, and make it to poor people in first world countries (though America's politicians would be safe).

An optimally evolved human disease would be one that could live in its host for years, and spread quickly and easily before its host died or was cured. Common cold spreads easily, but we fight it off to quickly. HIV can't be gotten our of our systems, but it takes too much to spreads it. There's a large number of bacteria commonly found on the skin that I think fit the bill the best, as they live happily on our skin and most people don't know about it at all. Things like staph, and the stuff that causes ringworm and athlete's foot. Those're there all the time. Yum.

Eureka!

I have been searching for a word for years, and I have finally found it! The word is antumbra, I found it thru a BBC article, and it means that part of the moon's (or another body's) shadow where an annular eclipse of the sun (or other light source) can be viewed. I'd already known the words umbra (for where you can see a total eclipse) and penumbra (partial), and I always suspected that there must be a special name for that section of the penumbra where you got a "reverse umbra," and finally I have found the word!

Oh yeah, it's taking place Monday Oct 2 for those of you in Europe, the "Near East" and Africa.

Science Words

Eleven parents of students at a Pennsylvania high school are suing over the school district's decision to include "intelligent design" -- an alternative to evolution that involves a God-like creator -- in the curriculum of ninth-grade biology classes.

The parents and the American Civil Liberties Union (ACLU) say the policy of the Dover Area School District in south-central Pennsylvania violates the constitutional separation of church and state, which forbids teaching religion in public schools.

The school board says there are "gaps" in evolution, which it emphasizes is a theory rather than established fact, and that students have a right to consider other views on the origins of life.

The problem in this story, and much of the "evolution is only a theory" story, is that English and Science are different languages that share a few words, but they mean different things. I figured I'd give a few definitions / explanations here of some words commonly used in the evolution versus ID argument.

Fact/Know/True
English: Something that is absolutely correct, beyond the shadow of a doubt.
Science: These terms are not generally used as their meanings are imprecise. Sometimes when talking w/ laypeople they're used to mean "observation," other times to mean "theory." When talking to other scientists we use different words. Nothing in science can be "known" absolutely as "true," so these words are meaningless.

Observation/Measurement
English: (self-evident)
Science: Data, numbers. This is the only stuff we "know" for "sure" is "true," and even then there can be mistakes in the scientist's methods to get the data. ("Data" is plural, "datum" is singular.) "Observation" is sometimes used to refer to the first step of the Scientific Method, which is also called "Question" at times.

Hypothesis
Science: An untested educated guess about the REASONS or explanation behind what's being experimented upon. May be proven correct or incorrect in the long run. Leads to predictions for specific experiments, and if consistently upheld leads to a theory.

Prediction
Science: A guess about the results of a particular experiment before we've done anything on it. Meaningless in the long term, because (1) it only applies to that specific experiment, and (2) it gets supplanted by data and theories.

Law
Science: A theory that can be expressed in simple terms, such as an easily memorized sentence, or a formula. I've seen many other definitions for the term Law, but this is the one I like. Some such "laws" have since been disproven, or were based upon faulty assumptions, but by tradition they are still called laws.

Theory
English: An untested guess at a reason, with a high chance of being wrong.
Science: A hypothesis that's been tested many many times for many years and hasn't ever been disproven. It's impossible to ever prove anything is absolutely "true" in science, as there is always the possibility of other explanations. A theory is the most likely one, and is as close to being "true" or "right" as scientists will ever admit. (Think of scientists as a non-committal boyfriend who won't say "I do." When he says "if I were going to marry anyone, it'd be you," that's like scientists saying "this is our theory, it hasn't been disproven yet.") Theories are often refined as time progresses, but rarely proven entirely wrong.

For example the geocentric solar system / universe proved wrong and was changed to the heliocentric model. It was refined when we determined the distance to stars, so we knew that the solar system was just part of the universe. Hubble further discovered (1923) that there were other galaxies than our own. Similarly, the reasons behind it all were refined, as Aristotle's "natural motion" turned into Galileo's inertia, Newton's gravity, and then Einstein's General Relativity (~1910). Further tweaks are continuing as Stephen Hawking and others study information in black holes and string theory.

Evolution is a good example of a theory still in the process of being refined at a coarser level. Where we are with evolution would be somewhere between Newton and Einstein with gravity, or between knowing the distance to stars and the distance to galaxies. Natural selection was presented before Darwin (I believe). Darwin extrapolated that, carried to extremes, natural selection could mutate species into other species, and that process was called evolution. During the 20th century it was recognized that there were distinct times when new species "quickly" (hundreds of thousands of years) developed, and this has been incorporated into an updated version of evolution called punctuated equilibrium (not often taught in K-12 schools, sadly). This refinement of the theory of evolution states that environemtnal triggers, such as massive habitat change brought on by a comet or asteroid collision, or ice ages or global warming, would cause "rapid" evolution of new species - faster than can be captured in the fossil record, but still gradual in terms of tens of thousands of generations.

Current-day theory about the geography of the universe is pretty solid. Current theory on gravity/GR (General Relativity) has a major gap, in that we can't yet reconcile GR with quantum mechanics. But we're working on it. Current theory on evolution is pretty solid but has some small gaps, in that we haven't found missing links from the evolutionary explosions, and some subsystems seem difficult to evolve in small steps. But we're working on it.

Steve's for Evolution

Denver, Colorado, February 16, 2003 -- A first-of-its-kind statement on evolution signed by over 200 scientists was unveiled today at the American Association for the Advancement of Science annual convention in Denver, Colorado, following Lawrence Krauss's topical lecture entitled "Scientific Ignorance as a Way of Life: From Science Fiction in Washington to Intelligent Design in the Classroom." The statement -- sponsored by the National Center for Science Education (NCSE), a nonprofit organization that defends the teaching of evolution in the public schools -- reads:

Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate scientific debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism of evolution. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to "intelligent design," to be introduced into the science curricula of the public schools.

The 220 signatories are a distinguished group. Almost all hold PhDs in the sciences. They include two Nobel prize winners, eight members of the National Academy of Sciences, and several well-known authors of popular science books such as Why We Age, Darwin's Ghost, and How the Mind Works.

And they're all named Steve.

More Evolution

The vast majority of working scientists contend that biological evolution is an established fact supported by overwhelming evidence. They say that evolution's mechanism is well explained by the process of random mutation and natural selection that Charles Darwin described 147 years ago. Darwin's theory - updated and confirmed by recent genetic discoveries - eventually will answer all or most questions about the origin and history of life, they say.

Nevertheless, polls repeatedly have found that a majority of Americans accept the concept of intelligent design and want it to be taught in schools along with evolution. President Bush waded into the debate in August, saying that schools should teach both.
...
Asked to cite scientific evidence for supernatural design, John Marburger, President Bush's science adviser, replied: "There isn't any. ... Intelligent design is not a scientific concept."

                                                            (Knight Ridder Newspapers)

ID-ers say that we have insufficient evidence to prove 100% conclusively that evolution is what formed life. That is a flawed argument. It's important to recognize that "lack of evidence" isn't the same as "contrary evidence."

For example, can you prove 100% conclusively that the sex of a person you know is female or male? The person may have secondary sex characteristics (such as breasts, muscles, or facial features) indiciative of a particular biologicial sex, but have you seen their primary sex characteristics (genetalia)? If so, there's still the possibility of that belying the individual's genetics, as in the case of hermaphrodites and individuals whom have undergone sexual reassignment surgery (aka a sex change operation). Have you taken a sample of their cells and looked at their chromosomes with a super-powerful microscope and counted the X's and Y's? That's the only way today to be certain of a person's sex, and yet I don't know a single person whose sex has been confirmed this way, and yet I still assert that I am female, my boyfriend is male, and for many other individuals I claim to "know" their sex.

If we are to accept that we need 100% conclusive evidence to accept evolution, we would have to also accept that we cannot know anyone's sex without analyzing their chromosomes.

   

Nothing's Inexplicable

No, we don't know everything yet, but we're continually getting closer. Take the core of Andromeda for example.

The Andromeda galaxy (aka M31) is our closest neighboring galaxy, and we think it's a lot like ours (the Milky Way). Eleven years ago we didn't know why the center was black, then the Hubble discovered it's a supermassive black hole. The next mystery was what's the blue glow around the center. Now Hubble's revealed that it's a disk of young blue giant stars. The disk is 1 light-year across and contains some 400 stars. Around that is a larger disk of old red stars about five light-years across (not sure how many of them).

To put things in perspective, the next star over from ours, Proxima Centauri (part of the Alpha Centauri system) is 4 ly away. And in the center of Andromeda there's 100 times that many stars in a diameter one fourth of that. We suspect the same thing is going on in the center of our own galaxy, as we've seen a number of bright blue stars there. Also if it were an uncommon thing, what's the chance that the only galaxy doing it would be the one next door? (That sort of ex post facto argument has flaws though, similar to the anthropic principle.)

Why is this freakish stuff going on in the core of a galaxy? We've no clue. But I bet we will in another 10 years. Maybe an IDer would say "God did it" and stop there, but not astronomers.

Armchair Science and Amateurs

There are few science fields where amateurs can make a contribution. One such field used to be in discovering new comets and asteroids, but now automated telescopes do the vast majority of the discovering. Amateurs still make a good contribution when they follow them with their own telescopes for a week after, but it's a bit less glamorous. Another case where they make a difference is tracking common birds at birdfeeders in Project Feederwatch.

However, amateur archaeology is a bit less common, and more so armchair archaeology, partly because of the training usually required, and I've never before heard of amateur satellite archaeology, but now some guy's done it, using Google Earth nonetheless. I wonder how many crackpot calls each museum gets compared to how many eventually pan out like this?

Ozone Hole

Read these articles about the present state of the ozone layer and ozone hole.

Ozone is a formerly hot topic, when they first discovered what was going down with it in the 80's. Today, we know a lot more about it, but fail to communicate this to the general public, as can be seen in the conflicting articles above. There are three aspects of ozone that should be discussed.

1.Ground Level Ozone

2.Stratospheric Ozone (Ozone Layer)

3.Depletion of Stratospheric Ozone (Ozone Hole)

First off, what is ozone in general? Ozone's chemical compound is O3 - it is made up of three oxygen atoms. Oxygen atoms can form up to two bonds with other atoms. Think of it like your typical person with two hands who can hold hands with up to two other people. If you and your sweetheart hold hands just with each other, right to left and left to right, you get the oxygen molecule, O2. When you hear about "breathing oxygen," this is what they mean. If you hold hands with two other people, and they each hold hands with each other, in a triangle shape, that's ozone. It's easier to break you three apart, to tear your hands from each other, as is true with ozone. Theoretically you could have O4 and so on, but these larger molecules get increasingly easy to break apart, increasingly unstable, and are pretty much never found in nature.

The next important aspect to ozone is that of UV light. Ultraviolet light is just the right energy to interact with ozone molecules, either forming or destroying the molecules. High up in the atmosphere, within the stratosphere, the ozone layer absorbs UV light when the UV breaks apart molecules. This protects all life on Earth from UV light, which causes cancer and various mutations. The molecules naturally reform on their own, so (without human interference) the amount of ozone in the ozone layer stays constant. Stratospheric ozone (the ozone layer) is good for humanity.

Low in the atmosphere, in the troposphere near the ground, not much ozone forms naturally. When UV light sneaks through past the upper layers and interacts with pollutants (such as nitrous oxide) it forms ozone. Not enough ozone to block UV light, so it doesn't do much good. But enough ozone to hurt us in other ways -- because it is so unstable, when you breathe ozone in, it interacts with the lining of your lungs and essentially "burns" (oxidizes) your lungs. This is especially bad for people with asthma or lung diseases. Tropospheric ozone (ground-level ozone) is bad for humanity.

To complicate matters more, not only does ground-level pollution help form ozone, other pollutants help destroy stratospheric ozone. Specfically, the chemicals that used to be used in air conditioners, chlorofluorocarbons (CFCs), interact quickly with ozone to break it apart, and then move on to break apart other ozone molecules. This contributed to the current day ozone hole. We have since banned CFCs, which is slowing the destruction of the ozone layer (destroying the ozone layer is the same as creating the ozone hole).

All that's fine and dandy, but it doesn't explain the flip-flopping results that CNN reports. As is often the case, I'm pretty sure it's all a matter of what they measured. The first group (that said the ozone layer is recovering) went to certain specific locations and measured how much ozone was in the ozone layer above those spots on the ground, for the dates 1996 to 2002. They are not up to date, and it's possible things have happened since then. The second group (ozone hole worst ever) measured specifically the size of the ozone hole over Antarctica this year. Perhaps this year was an anamoly?

I think most of the issue is in the locations chosen by both groups. It's possible that most of the ozone layer is getting thicker, but that one section of it over Antarctica is getting worse. What's the overall result if we combine the two groups? I don't know, and I don't think I could without looking at their data in depth and probably doing additional research. Give it a year or so and someone will do that and come up with a whole new set of answers. That's what's great about science -- no one person or group can claim to know what's "right"! :)

Believe

Main Entry: be·lieve
Pronunciation: b&-'lEv
Function: verb
Inflected Form(s): be·lieved; be·liev·ing
Etymology: Middle English beleven, from Old English belEfan, from be- + lyfan, lEfan to allow, believe; akin to Old High German gilouben to believe, Old English lEof dear -- more at LOVE
intransitive senses
1 a : to have a firm religious faith b : to accept as true, genuine, or real *ideals we believe in* *believes in ghosts*
2 : to have a firm conviction as to the goodness, efficacy, or ability of something *believe in exercise*
3 : to hold an opinion : THINK *I believe so*
transitive senses
1 a : to consider to be true or honest *believe the reports* *you wouldn't believe how long it took* b : to accept the word or evidence of *I believe you* *couldn't believe my ears*
2 : to hold as an opinion : SUPPOSE *I believe it will rain soon*

                               (Merriam-Webster Dictionary)

There is also an implication to the word "belief" that no evidence is required. Thus the CNN statement that "Astronomers believe a quasar is produced by cosmic gas as it is drawn toward the edge of a supermassive black hole" [emphasis added] is completely wrong. It implies that astronomers have no hard evidence and and are asserting it to be true for us to take on faith.

When you talk on the phone with your family, say your daughter, what evidence do you have that at the other end of your phone it's your daughter? The sound of her voice, the way she words her sentences. But you don't see her, do you? You can't touch her and know she's there. And yet you still know that it's her, right? That's how well astronomers know that quasars are produced in the system of a black hole.

We can't see the black hole directly, but we see all the evidence of one, for example, how fast the gas is moving and how far it is from the center indicates how much mass must be inside a certain radius, which tells us it must be a black hole. Computer models also show that the end of a super massive star's life is a black hole, and we'll see a disk and jets, which is what we see with quasars.

This isn't belief, it is our best knowledge.

"Telepathy Experiment"

It worked for you right? Unless you fscked up your math. It's a parlor trick, it's inevitable you'd get that answer, and here's why.

* Think of a number between 2 and 9
What number you choose is irrelevant, but for completeness, most people pick 7. This step seems to give an element of free will.

* Multiply the number by 9
* Add the two digits together
Anything from 2 to 9 multiplied by 9 gives a 2-digit number, with digits adding to nine. (Any multiple of nine has its digits add to a multiple of nine. It's a result of our base-ten number system, just numbers divisible by two have their last digit divisible by two, and similar rules for divisibility 3, 5, and 10. Oh and 7 as well, though I don't know anyone who has that test memorized.)
The result of these steps is 9 for everyone, eliminating the apparently random effect of the first stage.

* Subtract 5 from the number you now have
9-5=4, unless you're doing New Math.

* Convert the number into a letter -
4 = D

* Think of a European Country starting with that letter
There is exactly one country in Europe whose English name starts with the letter D, Denmark.

* Now think of the second letter of that country
E

* Think of an animal that starts with that letter
(This must be an animal - not a bird - so if you are thinking of an eagle think again!)
Again, for the record birds ARE a type of animal. I believe the author meant "mammal" where he put "animal."
There are a limited number of animals whose English names start with an E, or at least few well known ones. The ones I could think of are Eagle, Elephant, Emu. Birds are ruled out, leaving elephant.

* What colour is your animal?
Gray

** Now concentrate carefully on your answers
** Check below to see if I have read your mind

You are thinking of a grey elephant that comes from Denmark.

Asides from the misspelling of "gray," yeap, that's all you could come up with. QED

I'm sure similar tricks exist for other languages. Feel free to leave a comment explaining one you know of.

The Value of Life

Today I heard something in the Roberts confirmation hearings that disturbed me. OK, now I know this isn't directly about science, but it does touch on the "science vs. religion" debate that has been in the forefront of the American mind lately.

The Senate was questioning other individuals regarding the confirmation of Roberts as Chief Justice of the United States. I didn't catch the name of the woman being questioned, but she was a pastor. (If anyone knows her name, or where I can find a transcript of this particular discussion, please leave a comment and I'll update the info here.) Senator Jeff Sessions (R-AL) was discussing Wednesday's ruling in California that the Pledge of Alleigance was unconstitutional due to its current wording including the phrase "one nation under God."

The pastor said that she felt that the phrase "under God" was an affirmation of the speaker's religion, and therefore had no place in anything government-supported. Moreover, she said, the phrase was not original, as it was added well after the founding fathers, the framers of the Constitution, I think in the 1950's.

Sen. Sessions made a rebuttal statement that intrigued and disturbed me. The former was that the framers of the Constitution DID clearly believe in a Creator. He didn't make the specific quotation, but "...all men are created equal..." (Declaration of Independence) couldn't help but pop into my mind. Very intriguing. Quite likely, a "freedom from religion" never occurred to them, though that's not saying it would be inappropriate today.

He went on though. (Paraphrasing) "The framers of the Constitution believed in a Creator, and valued human life greatly because they believed we were specifically created. Today, Marxists, humanists, don't value human life as much. They can't."

I take offense at that assumption. In fact, I got pretty angry at him saying so. I value human life IMMENSELY and strongly oppose waging war. As I understand it, the war in Iraq was strongly supported by the Evangelical Christian Right. They believe in a God, a creator, and I don't. *GRRrrr...*

I belive life started by chance, and humans through evolution. Life is extremely precious to me because there was no gaurantee that it would happen at all. In fact, all the odds were stacked against it. The chance of us being here are billions of trillions to one against. Not only is life unlikely, but our very universe is moreso. The slightest tweaking of the laws of physics, and planets couldn't exist, stars couldn't exist, whole galaxies couldn't exist, or else the universe would've died soon after its birth.

Nothing and no one is looking out for us. Nothing cares if we all kill each other. The only thing looking down upon us is cold empty space. We are not special to anyone but ourselves. It is because of this that I feel it is all the more important for us to value every living human being.

A different form of dating

Scientists at Lawrence Livermore National Laboratories (LLNL) in California have debuted a new technique to determine the age of a tooth, and therefore the age of a body, and therefore narrow down the number of missing people to search through when identifying a corpse in a massive death situation such as New Orleans, the tsunami, or Sept 11.

Between 1955 and 1963 the US government performed atmospheric testing of nuclear bombs. This testing resulted in large amounts of carbon-14 (aka C-14, aka radiocarbon) being present in the atmosphere at the time. (As I understand the process, the fact that this isotope or version of carbon is radioactive is not used in the method.) This C-14 is nicely mixed throughout all the atmosphere of the world due to weather patterns. Much of this C-14 merged with a couple oxygens to form carbon dioxide, CO_2. The CO_2 was "inhaled" by plants and became part of their structure, so the same concentration of C-14 that is in the air can also be found in plants at that time. Additionally, the carbon that is in the plants is eaten by animals and goes into things like their muscles, so at any given time there's the same concentration of C-14 in the air, plants and animals.

Now, the concentration of C-14 in the air has been steadily decreasing, mostly due to the carbon mixing into the oceans. So that means that the amount of C-14 available in the air to go into plants and animals has been steadily decreasing. We know the rate at which it's decreasing pretty well empirically (i.e., from experiments) - you can think of it like we calibrated our C-14 / date conversion scale by testing on dead people's teeth.

And here come the teeth: Your adult teeth are formed before around age 8, and once they're formed they are fixed. You can't add or subtract any C-14.1 So how much C-14 was in the air when you were forming your teeth is how much C-14 will be in your teeth when you die. Forensic scientists can now work this process backwards: they get a set of teeth and take them to their lab and determine how much C-14 is in the teeth. This sets the date of tooth formation at a certain year, and therefore the date of birth at a certain year - plus or minus 1.6 years! That's much better than older methods of tooth ID, which gave plus or minus 10 years.

The only real catch is you have to have been younger than 8 when the atmospheric nuclear testing started, or not yet born. So if someone was born prior to 1943 that's all the test will be able to tell you, not how much earlier. But pretty nifty results for being irradiated with radioactive materials from nuclear weapons testing!

1 Those familar with radiocarbon dating probably took issue with this statement at first. In fact, C-14 does decay down to a steadier element, nitrogen-14, and relatively quickly. It only takes 5,730 years (±40) for half the C-14 in your teeth to turn into N-14. So in a lifetime of roughly 100 years you'll have around one sixtieth of a half life pass, or you'll have decayed away down to 98.85% of your original amount of C-14. Yeah, the passage of time doesn't make that much difference.

Note that the carbon dating in this case, that is the decrease in C-14 in the teeth is NOT due to radioactive decay, but the decreased amount of C-14 in the ecosystem.

Scientific Etiquette

In addition to operating by the Scienfitic Method or a variant thereof, scientists also follow an unwritten but well-known code of ethics. Some aspects of this code are familiar to all (the Hippocratic Oath, that doctors should help their patients), some are legally codified (human participants in studies have to be adequately informed of all risks), and there's even some borderline or as-yet-undecided ethics cases / topics that are policed by citizen watchgroups (animal testing, stem cell research).

One aspect of the scientific ethos is that of proprietary rights to data, especially important when related to pharmaceuticals and private funding. If one research group (under the auspices of an individual called the PI, principal1 investigator) is working on a certain drug, their data is private and no one else can legally access it without express written permission. Another group may be working on the same project independently, but the two are likely not allowed to collaborate, and thus it is simply a race against time to see whose work pays out, and who just wasted hundreds of thousands of dollars and years of work.

In astronomy, the best telescopes are majority-owned/-funded by the (US) government, and so the rules are different. Anything produced by our government or government funded is public domain -- eventually. Typically the researchers are granted proprietary rights ("ownership") to the data for a year, giving them a significant head start in analyzing the data and therefore publication. If they choose to publish sooner, as often happens, I believe only the things they put in the paper are publicly usable. After the year deadline has passed, any US citizen (and in practice, anyone in the world with computer access) may freely download and use the data as they see fit. This is why high resolution gorgeous Hubble Space Telescope images are freely available on the web. The data (images) were originally taken for some other purpose, but after the year was up, the HST publicity team cleaned them up and put them out there for anyone to see.

BUT, as your high school English teacher taught you, proper credit must always been given. The worst breach of etiquette physically possible is plagiarism, which can be anything ranging from unintentionally forgetting to list an author in your bibliography, to misleading others into thinking you did work that someone else did, to hacking into someone's computer and stealing their data.

As Dr. Michael Brown (Caltech) is accusing Dr. Jose-Luis Ortiz (Institute of Astrophysics of Andalusia, Granada), according to the New York Times. Ortiz's group is currently credited with discovering the outer solar system body known as 2003 EL61. (The object's fame was eclipsed by that of so-called "Xena," which actually is bigger than Pluto, so don't be surprised that you haven't heard of it.) Brown's group claims their three-month earlier discovery was digitally snooped on by Ortiz's group -- computers belonging to Ortiz, et al., surfed the web to a page listing where the Caltech telescope was pointed at on the key nights.

The accusation is that Ortiz (or his grad student) looked at those records of where Brown (or his grad student) had been looking, then Ortiz looked at his telescope's records and found images of the appropriate region of the sky in its history. Knowing that something special was there, and knowing that Brown worked on minor planet discoveries, Ortiz/grad student found the same object in their own images, but only because of the head's up from Brown's observations. 24 hours later Ortiz announces he's found the object now known as 2003 EL61. Soon after, Brown accuses Ortiz of failure to cite sources and demands he be stripped of discoverer status, and it be rightfully granted to Brown.

Ortiz counters with his own accusation of academic dishonesty by Brown. In the minor-planet-discovering community, there is a well known protocol for when you spot something new: you inform the International Astronomical Union's (IAU's) Minor Planet Center (MPC).

The MPC is the worldwide clearinghouse for planets, asteroids, comets, Kuiper Belt objects, Trans-Neptunian objects, Oort Cloud objects, 10th planets, and Planet X-es. If it's up there, in our Solar System, it isn't the Sun or man-made, and someone discovers it, the MPC is who you should tell. This is especially important for what's known as NEAs or NEOs: Near Earth Asteroids / Objects. Those are asteroids and other stuff that *might* *someday* have a chance of smacking the Earth, or (much more likely) having a near miss. This is one thing that Deep Impact got relatively right.

Say an astronomer discovers a new asteroid, comet, minor planet, whatever. Call that Night 1. He (or sometimes she) reports it to the MPC, along with details of when he saw it where. This can happen anywhere from Night 1 to Night 30 if he's lazy. I'll call it Night 2. By the end of the day, or sometimes the hour, the MPC calculates a rough orbit for it, and determines where it should be visible in the sky in the future. When they calculate the rough orbit, red flags go up if it's an NEA. In this case, emails IMMEDIATELY go out to major observatories and astronomers (both professional and amateur) who've elected to be on the list. This also happens if it's not an NEA, but without the red flags. Night 3 dozens to hundreds of telescopes point to the expected location in the sky, and the media catches wind of the story and it runs on front pages. Day 3 - Night 4, resulting data is sent back to the MPC. Sometimes it was a bogus detection of an object and nothing is found Night 3, and the search is called off. More often, the MPC refines its calculations and repeats the request for observations. By the end of Night 5 someone has found archived images from five or ten years ago that had the object in it, but no one realized at the time. Around a week after the initial detection, the orbit has been refined enough to know that the asteroid isn't going to hit the earth in 3 weeks, or a million years, whatever the original worry was. Papers are published by a few astronomers within a few months.

Brown didn't do this. He didn't send the initial detection to the MPC because he didn't want some other group scooping his story. Which happened anyway. But if he had told the MPC, then Ortiz wouldn't've had a leg to stand on. But if Brown had then anyone could've published on it by now. But it's Brown's tendency to be secretive that prompted Ortiz to commit the information theft. If he did. Or his grad student.

Conclusions:
1) Bad blood begets more bad blood.
2) Shit, I thought astro was free of this sorta crap.

Falsafiabilty

Science is based upon a process known as the Scientific Method. All science uses a modified form of this.

1.Obersvation / Question - the scientist observes (notices) something s/he wants to learn more about, or comes up with a question he wants answered. For example, it rains on cloudy days. Why does it rain on cloudy days?

2.Hypothesis - a guess as to the reason behind what he observes. The clouds are made of Super Crows, and when they shit it rains.

3.Prediction - subtly different from hypothesis, it is the testable results expected if your hypothesis is true. If I look at a cloud with a telescope, I should be able to see the Super Crows.

4.Experiment - carrying out the test implied by your predictions

5.Conclusion - assessing whether you were right, how good the experiment was, etc. I didn't see any Super Crows, but I accidentally left the cap on the telescope, so I think that's why, and I need to try again.

You'll note that the key to this whole process is the ability to perform a test, experiment, or observation that can verify or deny your hypothesis. Some things are impossible to test, or impossible to prove false. There is a pink elephant somewhere on Earth. It's really damned hard to go everywhere on the Earth, and even if you could and you missed him, maybe he snuck to Nepal while you were in Japan, and then snuck back to Japan when you left for Antarctica. Johnny's got a crush on Melissa. You ask him if he's got a crush on her. If he says yes, you've proven your hypothesis true. If he says no, he's in denial to himself, or isn't admitting it to you, proving your hypothesis true. It's impossible to prove your hypothesis false.

Either of these cases are unfalsifiable - impossible to prove false through an experiment. A whole class of things that fall under "unfalsifiable" are the supernatural, including any higher powers and their effects, such as God, Creationism, and Intelligent Design (ID). I'm not saying ID is wrong, I'm saying it's untestable. There is nothing we can do to determine whether God created Adam and Eve, or just helped evolution along, or even only started the ball rolling with the Big Bang and then took a seat in the sidelines (sometimes called the Clockmaker Hypothesis).

•Science requires the process of testing.

•ID is impossible to test.

•Logical conclusion: ID has no place in science.

Once again, just to make sure you get it, science does not say Intelligent Design is wrong, science says it is unable to say anything about it. Science admits a total failure to address the issue of God, and leaves it to the churches, the atheists, and the ACLU to duke out.

Assumptions: a practical guide

Late last week I noticed a few harmless yellowjackets on the inside of my office window screen. Today I was stung by one of the insects in the process of leaving my office. Which leads me to evaluate the assumptions in my initial statement, "harmless yellowjackets." Either (a) yellowjackets were/are not harmless, and/or (b) they were not yellowjackets, but hornets or wasps. Sometimes it's hard to determine what assumptions you have made until something proves you painfully wrong. I'd been told since childhood by my family that yellowjackets are harmless, and I've never been afraid of them.

There IS a difference between the three bugs, yellowjackets, hornets, and wasps, not that I understand insects or species classification well enough to know the difference, and Wikipedia is little help as they all have different tables (you'll see my comments requesting that be fixed in their discussion sections w/in a few mintues of this posting), but all three sting. Even so, I am unable to identify the bug now, as it was crippled by my hand crushing it on the doorknob and put out of its misery by the retributive depths of my sole, and there were not enough remains for a thorough autopsy.

The next thing I got to test in this encounter after my assumptions, was my allergies. In my childhood I was allergic to bee stings. Most stings would merely result in massive swelling and occasional puffy eyes. If the stinger remained in my skin, I would start having difficulty breathing until the stinger were removed with tweezers. Since then, I have developed asthma (though mild), but simultaneously my allergies have weakened. Additionally, I have never been stung by a wasp/hornet/yellowjacket. This of course means that I had WAY too many independent variables (asthma, allergies, age, type of bug) of which I was simaltaneously testing the effect on the dependent variable (my ability to breathe), and no good control. I still stand by my reported results (survival, no reaction other than the normal one of PAIN), but I must repeat the experiment in a more controlled environment (allergy tests) to determine causality of survival and estimate future mortality rate.

Question Everything

Especially if it comes to you in email. Skepticism is thoroughly scientific, despite Fox Mulder's questioning the wrong things. ;)

•Have you seen gorgeous pictures of hurricane Katrina approaching a town in Mississippi? Did you notice that the ground's all farmland? And that the "eye" area is much too small for the typical "clear, calm, and sunny"? If so, you've got the key points that

•Did you know that in September of 2005 Mars is going to approach so close that it'll be bigger than the Moon? Did you notice that the same email went out in 2003? Did you stop and think that if Mars were actually close enough to the Earth that it were as big as the Moon, that its gravity would probably be stronger than the Moon's and we'd have killer tides worse than the December 2004 tsunami or August 2005 hurricane Katrina? Did you read the explanation that it's a recycled email with a typo in the original?

•Fwd: Fw: virus alert - WORST VIRUS EVER ---CNN ANNOUNCED -- PLEASE SEND THIS TO EVERYONE ON YOUR CONTACT LIST !! Aw man, there's more of these than I can list... Read my post on it for a summary of how to know if it's a real virus or a hoax, and how to best prevent yourself from getting virii all around.

Here's what I do when I get a forwarded email that seems a bit sneaky.

1.Go to Google and look up keywords in the email. Examples for the three above might be "Katrina hurricane photos", "Mars moon telescope", and "virus alert 'card for you' ".

2.Google will give you many hits; look for sites that you personally believe to be reliable. I trust CNN, BBC, the NY Times, Boston Globe, Washington Post for news; Sophos, Symantec, MacAfee, Norton for virus; Snopes for general urban legends.

3.Read or skim at least two or three of your "trustworthy" hits. If they agree with each other, then I will consider them all true.

4.Compose a well-reasoned reply/rebuttal to the individual explaining why the forwarded email is faulty. I am sure to include the references I used so they can independently verify it. Suggest they follow a similar line of attack next time they receive an email like that one.

5.If the person CC'd others, I also CC them on my reply, and ask that they put me on BCC (blind carbon-copy) for mass emails when applicable, so that spammers don't find my email address in the future, and so that when one of the others does receive a virus they don't have me in their address book. (If they don't know enough to avoid hoaxes, they probably don't know enough to avoid real viruses.)

6.Send. Delete original. Rant. Repeat as necessary.

Have you been taken in by an email hoax? Or is there one you didn't understand the explanation of? Let me know!

Most distant gamma ray burst detected

The Swift telescope has detected - and studied - the most distant gamma ray burst ever. Gamma ray bursts (GRBs) are currently believed to be created when a massive star collapses into a black hole. I'm not sure what's the difference between this and a star going supernova, so I'll be researching that on Wikipedia next.

It has a so-called "redshift" of 6.29, which translates to a distance of about 13 billion light years from Earth. ... "This burst smashes the old distance record by 500 million light years," said Dr Daniel Reichart of the University of North Carolina, who has been leading the measurement of its distance.
How do we know it's the farthest? Determining the distance to astronomical objects was one of the most important discoveries of the 20th century. Edwin Hubble (after whom the Hubble Space Telescope is named) discovered that galaxies that are farther away from us (based upon earlier measurements of distance) are also moving away from us faster (greater speed). The speed is directly measured by the Doppler Effect / Shift - the same thing that makes the siren of an abulance driving past change in pitch. In GRBs and other things in the sky, we measure how the color of the light changes and use this to determine the velocity, which cosmologists translate into redshift. The velocity to redshift conversion is exact; the redshift or velocity to distance conversion is still under debate. The current best guess is 71±4 (km/s)/Mpc.

The Swift telescope used in this study can actually detect GRBs even farther away than that, if they happen. Light takes a while to get here, so when you look at objects far away, you're looking at long ago in the past. Think about sending letters by snail mail. If you send one in the same town, it might get there the same day, so if you get a letter from the same town, the person probably wrote it about the day before. If you get a letter from a few states away, the letter's a few days old. A letter from the other side of the country might be a week old, and any news it has will be that long out of date. Even farther away, a letter from Europe would take a couple weeks.

Swift can see very dim objects, dim = far away = long ago = soon after the Big Bang (200 million years after, they guess). We don't yet know how soon after the Big Bang stars started to form. If there were no stars, then none of them would've been dying and forming GRBs! Can you imagine a universe that hasn't yet formed stars?

Modern Cars

As I'm sure we're all sick of hearing by now, the last time gas cost this much (adjusted for inflation) was in 1981. At the time, cars got 21 mpg. Today, the average car gets 21 mpg. No, that's not a typo. Despite all the wonders of technology, today's cars have the same fuel efficiency as they did 24 years ago. Why is that? SUVs. The increased weight (and probably air resistance too) make up for the best the automotive industry decided to dish out in fuel efficienct technolgy.

Despite making that good point, the article upon which I based this post goes on to throw meaningless numbers at the reader.

Light trucks, a category that includes SUVs and minivans, now account for 50 percent of passenger vehicles sold in the U.S. That's more than double their share in 1981.1
...
Large SUV sales are 11.2 percent lower than they were at this time last year, according to AutoData.2
...
Top speed has also increased from 112 miles per hour in 1981 to 136 mph today.3
...
Overall, the basic 5.7 liter Hemi V8 engine is about 10 percent more efficient than the engine it replaced. The addition of "multi-displacement" technology, which shuts off four cylinders when their power is not added, as in steady highway cruising, boosted efficiency by another 10 percent.4

1.Do they mean double the percentage from 1981, or double the raw number from 1981? The former is more meaniningful, as simple increase in purchasing will change the latter without showing if people prefer SUVs or cars.

2.Ditto, but more so: percent of vehicles sold, number of vehicles sold, percent of dollars spent, amount of dollars spent? Amount of dollars spent would decrease if they simply decreased the price of SUVs.

3.From context, they mean average top speed, not top top speed, but still, who really drives their cars at top speed?

4.Hey wait a sec, they just said it increased by 10% overall, and then they said it was an additional 10% on top of that? That's not even a mistake I'll let my developmental math kids get away with. On the other hand, maybe they meant that the engine just by itself is 10% more efficent, and the "multi-displacement technology" makes it 10% more efficient on top of that. If so, it's even more a case of sloppy reporting - the description didn't really say that, and for that second 10%, 10% of what?, the original engine or the modified engine? (Though it doesn't matter order-of-magnitude, science reporters rarely understand that concept.)

This isn't even a science article, it's a cars article, and the little evidence they throw in to try and make it more scientific goes away.

"Modern Science" launches!

Welcome to yet another blog... This one's going to be about science today: new discoveries, debunking pseudoscience, and controversies. If you have a question about something in science, leave a comment and I'll try to address it. I encourage debate in the comments section - but no name-calling!
To start the ball rolling, I'd like to draw your attention to the tendancy of poor reporting on science in the media. The Guardian recently ran a good article discussing it. This article was brought to my attention by sclerotic rings, where I mentioned that I recently saw a CNN article on a computer virus that'd taken down the station, and their own slow response to fix it. In the very same article criticizing their own reactions, they interviewed MANY newscasters and behind-the-scenes people laughing and joking about not knowing what a worm is. "Hah hah, it's okay to not have a clue what's going on!"

           I think this eroding of science in the media is leading to a general disrespect for the method and results of science in the general public in the US, thus allowing non-scientific ideas to take root, such as astrology, the Moon Landing Hoax conspiracy theory, and Intelligent Design (ID).

Discuss.
Expect me to say "prove it."

Induced pluripotent stem cells

It was one of the top science stories of 2007: number 2 on Science's list – reprogramming ordinary adult body cells (of mice and humans) to act like embryonic stem cells.

The riddle of Dolly the Sheep has puzzled biologists for more than a decade: What is it about the oocyte that rejuvenates the nucleus of a differentiated cell, prompting the genome to return to the embryonic state and form a new individual? This year, scientists came closer to solving that riddle. In a series of papers, researchers showed that by adding just a handful of genes to skin cells, they could reprogram those cells to look and act like embryonic stem (ES) cells.

The story really began in October 2006, when a team at Kyoto University in Japan, led by Shinya Yamanaka, announced that they had reprogrammed mouse skin cells into cells that closely resembled embryonic stem cells, based on certain characteristic genes that were expressed. The reprogramming was done by introducing genes for four important stem cell transcription factors (Oct4 (or sometimes the similar Oct3), Sox2, c-Myc, and Klf4) into the skin cells with the help of a genetically engineered retrovirus.

But the team could not at that time demonstrate that these reprogrammed cells would differentiate into a variety of adult cells after having been introduced into a mouse embryo which then developed into an adult mouse. Being able to do this would verify the pluripotency of the reprogrammed cells. (Pluripotency is the ability of a cell to develop into any type of fetal or adult cell. It is characteristic of embryonic stem cells.) The reprogrammed cells are called induced pluripotent stem (iPS) cells.

However, in June 2007 Yamanaka's team, along with two others, reported that they had been able to provide the missing demonstration of pluripotency. The second team that joined in reporting this accomplishment was led by Rudolf Jaenisch at MIT's Whitehead Institute for Biomedical Research. The third team was led jointly by Konrad Hochedlinger of the Harvard Stem Cell Institute and Kathrin Plath of the UCLA Institute for Stem Cell Biology and Medicine.Recently (mid-February), Kathrin Plath's team at UCLA has also announced success in reprogramming human skin cells, using the same techniques as previously reported. They have also verified that the induced pluripotent cells are very similar to embryonic stem cells:
Human Skin Cells Reprogrammed Into Embryonic Stem Cells

                                                       The reprogrammed cells were not just functionally identical to embryonic stem cells. They also had identical biological structure, expressed the same genes and could be coaxed into giving rise to the same cell types as human embryonic stem cells.

As we've noted, there have been some potential problems with the work already mentioned. First, any process that activates c-Myc (directly or indirectly) runs risks of promoting cancerous tumors. Second, the processes have used retroviruses to introduce the necessary genetic material into cells to be reprogrammed. This also runs the risk of inducing cancer.

So Konrad Hochedlinger's team has come along with work in mice to reduce or remove these cancer-causing risks:
Discovery Could Help Reprogram Adult Cells To Embryonic Stem Cell-like State

                                                 Harvard Stem Cell Institute (HSCI) and Massachusetts General Hospital (MGH) researchers have taken a major step toward eventually being able to reprogram adult cells to an embryonic stem cell-like state without the use of viruses or cancer-causing genes.

In a paper released online today by the journal Cell Stem Cell, Konrad Hochedlinger and colleagues report that they have discovered how long adult cells need to be exposed to reprogramming factors before they convert to an embryonic-like state, and have “defined the sequence of events that occur during reprogramming.”

This work on adult mouse skin cells should help researchers narrow the field of candidate chemicals and proteins that might be used to safely turn these processes on and off. This is particularly important because at this stage in the study of these induced pluripotent (iPS) cells, researchers are using cancer-causing genes to initiate the process, and are using retroviruses, which can activate cancer genes, to insert the genes into the target cells. As long as the work involves the use of either oncogenes or retroviruses, it would not be possible to use these converted cells in patients.

And hard on their heels, other teams are announcing similar findings:

Stem cell breakthrough may reduce cancer risk

                       The main obstacle to using "reprogrammed" human stem cells – the danger that they might turn cancerous – has been solved, claims a US company.

PrimeGen, based in Irvine, California, says that its scientists have converted specialised adult human cells back to a seemingly embryonic state – using methods that are much less likely to trigger cancer than those deployed previously.

The company also claims to be able to produce reprogrammed cells faster and much more efficiently than other scientists.

Alternative energy sources

The outlook on energy alternatives to fossil fuels is looking a little bleak.

There have been several recent studies or reports casting significant doubt on the economic and/or environmental viability, at least for the near and intermediate future, of some of the leading contenders to supplant fossil fuels.

First up: nuclear power. Of course, environmentalists and others have had grave doubts about nuclear for decades, because of problems with safe disposal of spent nuclear fuel and the dangers of diversion of enriched uranium to manufacture of weapons. On top of that, there is the argument that replacing generation of power from burning fossil fuels with generation from nuclear sources may well contribute more to release of CO2 into the atmosphere than continuing to use fossil fuels. This comes about because so much power (generated from burning of fossil fuels) will need to be expended simply to build from scratch many new nuclear power plants and sharply increase the mining and purification of uranium:
Nuclear Power Not Efficient Enough To Replace Fossil Fuels, Study Finds

                                               Nuclear energy production must increase by more than 10 percent each year from 2010 to 2050 to meet all future energy demands and replace fossil fuels, but this is an unsustainable prospect. According to a report published in Inderscience's International Journal of Nuclear Governance, Economy and Ecology such a large growth rate will require a major improvement in nuclear power efficiency otherwise each new power plant will simply cannibalize the energy produced by earlier nuclear power plants.

Here's another way to look at this. If you consider just the marginal costs of producing a kW of energy from nuclear fuel vs. fossil fuel – counting (if you can) both direct economic costs and costs due to release of CO2 into the atmosphere – nuclear energy might be superior. However, if you also consider the capital expense (both direct and indirect) required to build enough new nuclear facilities to replace existing conventional facilities and also meet increased demand, then (according to the study) nuclear loses.

So what about using other energy sources as alternatives to fossil fuels, in order to significantly reduce dependency on fossil fuels and release of CO2? Like hydrogen, for example. Of course, this depends on further developing a lot of technology that's either not cost-competitive yet (fuel cells) or not even available yet (practical and safe means of storing and transporting hydrogen). To say nothing of the capital costs (as above) needed to build hydrogen infrastructure if and when the technology is available.

Even if technology can solve the difficult problems of storing and transporting hydrogen, there's another fundamental problem. Hydrogen itself is more of a form of energy suitable for transport and storage than it is a readily available source of energy (like sunlight or fossil fuels) that can be acquired or extracted (relatively) cheaply. There's no hydrogen just sitting around (like natural gas) waiting to be mined and distributed. Energy has to be consumed in order to separate hydrogen from oxygen, which together make up H2O. This energy has to come from some other source, as input to the electrical/chemical process that separates out hydrogen (or recombines it to make another fuel such as methane). This energy is regained later – but always with some percentage loss – when hydrogen is chemically recombined with oxygen (as in a fuel cell).

There really isn't any energy advantage to hydrogen at all, except for the (presumed) advantage over batteries in storage and transport. Of course, energy in a storable form is required for use in vehicles like cars and airplanes, in spite of the unavoidable losses along the way. The following essay goes into all of this in more detail.
The Hydrogen Economy

                                          Skeptics scoff at perpetual motion, free energy, and cold fusion, but what about energy from hydrogen? Before we invest trillions of dollars in a hydrogen economy, we should examine the science and pseudoscience behind the hydrogen hype.

There are some problems with the essay. First, one does not "make" hydrogen. It is extracted from chemical compounds like water, hydrocarbons (fossil fuels except coal), or biomass (carbohydrates, cellulose, etc.). Energy has to be input to the process in order to break the chemical bonds between hydrogen and other elements (carbon or oxygen). You get the energy back out when hydrogen recombines with oxygen or carbon (in a fuel cell, combustion chamber, etc.) – but always at some loss.

Second, the essay mostly assumes hydrogen will be stored and transported in liquid form, which is difficult and expensive, since liquid hydrogen boils at an ultracold -253°C. There is some hope that technology can be developed to store gaseous hydrogen in exotic solid materials at reasonable temperatures and pressures. However, at this point that's still conjectural. The larger point is that a practical "hydrogen economy" is still, at best, not in the near future.

Saturday, March 15, 2008
Alternative energy sources
The outlook on energy alternatives to fossil fuels is looking a little bleak.

There have been several recent studies or reports casting significant doubt on the economic and/or environmental viability, at least for the near and intermediate future, of some of the leading contenders to supplant fossil fuels.

First up: nuclear power. Of course, environmentalists and others have had grave doubts about nuclear for decades, because of problems with safe disposal of spent nuclear fuel and the dangers of diversion of enriched uranium to manufacture of weapons. On top of that, there is the argument that replacing generation of power from burning fossil fuels with generation from nuclear sources may well contribute more to release of CO2 into the atmosphere than continuing to use fossil fuels. This comes about because so much power (generated from burning of fossil fuels) will need to be expended simply to build from scratch many new nuclear power plants and sharply increase the mining and purification of uranium:

Nuclear Power Not Efficient Enough To Replace Fossil Fuels, Study Finds

Nuclear energy production must increase by more than 10 percent each year from 2010 to 2050 to meet all future energy demands and replace fossil fuels, but this is an unsustainable prospect. According to a report published in Inderscience's International Journal of Nuclear Governance, Economy and Ecology such a large growth rate will require a major improvement in nuclear power efficiency otherwise each new power plant will simply cannibalize the energy produced by earlier nuclear power plants.

Here's another way to look at this. If you consider just the marginal costs of producing a kW of energy from nuclear fuel vs. fossil fuel – counting (if you can) both direct economic costs and costs due to release of CO2 into the atmosphere – nuclear energy might be superior. However, if you also consider the capital expense (both direct and indirect) required to build enough new nuclear facilities to replace existing conventional facilities and also meet increased demand, then (according to the study) nuclear loses.

So what about using other energy sources as alternatives to fossil fuels, in order to significantly reduce dependency on fossil fuels and release of CO2? Like hydrogen, for example. Of course, this depends on further developing a lot of technology that's either not cost-competitive yet (fuel cells) or not even available yet (practical and safe means of storing and transporting hydrogen). To say nothing of the capital costs (as above) needed to build hydrogen infrastructure if and when the technology is available.

Even if technology can solve the difficult problems of storing and transporting hydrogen, there's another fundamental problem. Hydrogen itself is more of a form of energy suitable for transport and storage than it is a readily available source of energy (like sunlight or fossil fuels) that can be acquired or extracted (relatively) cheaply. There's no hydrogen just sitting around (like natural gas) waiting to be mined and distributed. Energy has to be consumed in order to separate hydrogen from oxygen, which together make up H2O. This energy has to come from some other source, as input to the electrical/chemical process that separates out hydrogen (or recombines it to make another fuel such as methane). This energy is regained later – but always with some percentage loss – when hydrogen is chemically recombined with oxygen (as in a fuel cell).

There really isn't any energy advantage to hydrogen at all, except for the (presumed) advantage over batteries in storage and transport. Of course, energy in a storable form is required for use in vehicles like cars and airplanes, in spite of the unavoidable losses along the way. The following essay goes into all of this in more detail.

The Hydrogen Economy

Skeptics scoff at perpetual motion, free energy, and cold fusion, but what about energy from hydrogen? Before we invest trillions of dollars in a hydrogen economy, we should examine the science and pseudoscience behind the hydrogen hype.

There are some problems with the essay. First, one does not "make" hydrogen. It is extracted from chemical compounds like water, hydrocarbons (fossil fuels except coal), or biomass (carbohydrates, cellulose, etc.). Energy has to be input to the process in order to break the chemical bonds between hydrogen and other elements (carbon or oxygen). You get the energy back out when hydrogen recombines with oxygen or carbon (in a fuel cell, combustion chamber, etc.) – but always at some loss.

Second, the essay mostly assumes hydrogen will be stored and transported in liquid form, which is difficult and expensive, since liquid hydrogen boils at an ultracold -253°C. There is some hope that technology can be developed to store gaseous hydrogen in exotic solid materials at reasonable temperatures and pressures. (Recent examples: here, here.) However, at this point that's still conjectural. The larger point is that a practical "hydrogen economy" is still, at best, not in the near future.

So hydrogen is not an energy source, and it is even very problematical as a way to store energy in a portable form for use in cars and airplanes. Fortunately, there are other ways to make energy portable, such as batteries. A Toyota Prius uses nickel metal hydride batteries to store energy from the regenerative braking system, and it seems to be an economically successful product. Lithium ion batteries, such as are used in laptop computers, have a higher energy density than the nickel metal hydride type. They have problems of their own, but significant improvements are being made. (See here, here, here.)

That still leaves the problem of developing additional actual sources of energy, that are alternatives to fossil fuels. Ethanol (grain alcohol) is getting a lot of publicity these days. It's politically popular with the agricultural industry, for obvious reasons. Ethanol partially solves one problem with fossil hydrocarbon fuels – by removing some dependence on politically unstable areas as a fuel source. But ethanol does nothing for the problem of CO2 emissions.

And it creates serious problems of its own, such as driving up the cost of agricultural products needed to feed people. Further, as with hydrogen, it takes a lot of energy to extract ethanol (or other energy carriers such as other biofuels or methane) from agricultural crops or biomass. Critiques of ethanol and other biofuels are not new, though they don't seem to get the attention they deserve.

               Other alternatives? There's always solar (photovoltaic) energy. Of all new but currently available alternative energy sources to fossil fuels (whether oil, natural gas, or coal), solar seems to be the most economical, especially taking reduced CO2 emissions into account.

But of course, solar also has its problems too. These include capital costs for building infrastructure to capture solar energy and to store it (for peak or nighttime use) or transmit it from the sunniest areas with low land prices. It's these capital costs (initial construction and eventual replacement) that hurt, since the marginal cost of each kWh is almost nil.

However, making detailed economic comparisons with traditional energy sources is rather difficult, as this study argues: Cloudy Outlook For Solar Panels: Costs Substantially Eclipse Benefits.

It would seem that the real difficulty of economic analysis lies in predicting the future costs of conventional energy sources – fossil fuels, especially oil. Some of the problems:

•How to estimate costs associated with CO2 emissions, given that the idea of global warming itself is so controversial (especially in the minds of economists and political officials, if not atmospheric scientists). To say nothing of estimating social costs of conjectural side effects, such as sea level rise, serious water shortages, detrimental impact on human and animal health, impact on agricultural production, etc.

•How to estimate the foreseeable rise in price of fossil fuels (especially oil) due to political instability, rising extraction costs (deep ocean sources), depletion of supplies, and rapid increase in demand from developing parts of the world. (There are large uncertainties in all of these factors, and some cost has to be allocated to this uncertainty itself.)

•How to handle the issue of proper pricing for energy at times of peak demand, as opposed to off-hours. (The report just mentioned discusses this.)

At present, the cost of solar energy, taking into account such things as installation costs, depreciation, etc., might well be two to four times the cost of energy from fossil fuels. But at least the cost of solar is pretty certain to decline, while the cost of energy from fossil fuels can only increase – and at a worrisomely unpredictable rate, in view of the uncertainties just listed.

 

Embryonic stem cells and Klf4

There's now some additional information on one of the transcription factors written about here, which are able to reprogram adult skin cells into embryonic stem cells. To review, one of the teams responsible for this research used Oct3/4, Sox2, c-Myc, and Klf4 for the reprogramming, while another team used Oct3/4, Sox2, Nanog and Lin28.

Of the transcription factors in the first list, all but Klf4 have been well-studied. So it is of some interest to know more about Klf4, and why it seems to be somewhat less essential than the others.

Some of the interesting details are reported on here: Molecular Alliance That Sustains Embryonic Stem Cell State Identified.

Klf4 is normally active in real embryonic stem cells. To investigate the role Klf4 might be playing in the reprogramming of skin cells, the researchers investigated embryonic stem cells that had been artificially depleted of Klf4. To their surprise, the team found that the cells maintained their pluripotency.

The question then was how to explain this. What was found is that two closely-related transcription factors – Klf2 and Klf5 – took over the role of Klf4:

"Most important, the data showed that the other Klfs were bound to the target sites when one of them was depleted." said Dr. Ng. "These Krüppel-like factors form a very powerful alliance that work together on regulating common targets. The impact of losing one of them is masked by the other two sibling molecules."

This family of transcription factors, called Kruppel-like factors, gets its name from a homology to the Drosophila Krüppel protein. Members of this family have been studied for their roles in cell proliferation, differentiation and survival, especially in the context of cancer.

Interestingly enough, according to the research press release,

Klfs were found to regulate the Nanog gene and other key genes that must be active for ES cells to be pluripotent, or capable of differentiating into virtually any type of cells. Nanog gene is one of the key pluripotency genes in ES cells.

"We suggest that Nanog and other genes are key effectors for the biological functions of the Klfs in ES cells," Dr. Ng said.

"Together, our study provides new insight into how the core Klf circuitry integrates into the Nanog transcriptional network to specify gene expression unique to ES cells.

Nanog, of course, is one of the transcription factors in the set of transcription factors which was found to be an alternative, for reprogramming adult cells, to the set that contained Klf4.

The Nanog protein, too, is known to be critically important in pluripotent stem cells. It is a homeobox transcription factor that appears to play an essential role in self-renewal of undifferentiated embryonic stem cells. It also appears to be connected with cancer, because (according to Wikipedia) "It has been shown that the tumour suppressor p53 binds to the promoter of NANOG and suppresses its expression after DNA damage in mouse embryonic stem cells. p53 can thus induce differentiation of embronic stem cells into other cell types which undergo efficient p53-dependent cell-cycle arrest and apoptosis."

The connection of Klf proteins with cancer is not only through Nanog. According to Wikipedia, "Klf4 also interacts with the p300/CBP transcription co-activators." The closely-related p300 and CBP "interact with numerous transcription factors and act to increase the expression of their target genes." And they too are involved with cancer:

Mutations in the p300 gene have been identified in several other types of cancer. These mutations are somatic, which means they are acquired during a person's lifetime and are present only in certain cells. Somatic mutations in the p300 gene have been found in a small number of solid tumors, including cancers of the colon and rectum, stomach, breast and pancreas. Studies suggest that p300 mutations may also play a role in the development of some prostate cancers, and could help predict whether these tumors will increase in size or spread to other parts of the body. In cancer cells, p300 mutations prevent the gene from producing any functional protein. Without p300, cells cannot effectively restrain growth and division, which can allow cancerous tumors to form.

What IQ-1 does, Kahn explains, is to block one arm of a cell-signaling pathway called the Wnt pathway, while enhancing the signal coming from the other arm of the Wnt pathway. The Wnt pathway is known to have dichotomous effects on stem cells i.e. both proliferative and differentiative. More specifically, IQ-1 blocks the coactivator p300 from interacting with the protein ß-catenin; this prevents the stem cells from being 'told' to differentiate into a more specific cell type.

Cheating

It's certainly appropriate – as well as hilarious – to draw the analogy between humans and slime molds. Kurt Vonnegut, Samuel Clemens, and H. L. Mencken would approve. But there's serious truth in it:

Some cheaters can keep it in their genes

                               A new study examining social behaviour suggests certain individuals are genetically programmed to cheat and often will do- providing they can get away with it.

The researchers looked at slime moulds - microscopic single-cell organisms or amoebae that are forced to cooperate with one another when food is in short supply. Studying slime moulds at the cellular level provides the scientists with a unique insight into the genes that may also influence human behaviour.

The international team, including biologists from The University of Manchester, found that some amoebae have the ability to use cheating tactics to give them a better chance of survival. The research - published in the journal Nature - not only demonstrates that cheating is a natural phenomenon governed by our genes but that it may be widespread among social creatures.

This is familiar territory. I wrote about it here, where the subject (among other things) was the evolutionary origins of altruism and cooperation. One needs to read that (or be familiar with the viewpoint of evolutionary psychology on the origins of morality and ethics) in order to see how the following speculations fit in.

Apparently, in many social species, there is a tendency for populations to evolve with an equilibrium mixture of cheaters and non-cheaters ("altruists"). Although cooperation increases the probability of group survival, some individuals in any group can gain an advantage by cheating, so they will tend to persist in groups as time goes on. But they can't become too numerous without harming the group's survival. So eventually some equilibrium is reached.

In the simulation of intergroup warfare I discussed in my earlier post, it was the warfare which worked against survival, so that under such conditions, there were pressures against a large equilibrium fraction of cheaters. These pressures were manifested in such things as religion and moral/ethical codes of behavior, together with formalized punishment of cheaters.

But warfare isn't the only factor that can put pressure on group survival. Simply living in a hostile or marginal environment can do it. This seems to be what happens with slime molds. Individuals can be, well, individualists until there is an existential threat.

One wonders whether this isn't what happened to the Neanderthals. Their environment was harsh. They must have migrated to that environment during favorable conditions (otherwise, why stay?), but eventually conditions got worse. If they were not able to evolve (biologically and/or socially) fast enough to reduce the percentage of cheaters, it's reasonable to suppose all would die. Modern humans living around the same time in similar environments – and who survived – perhaps were able to evolve faster. Or else they had already better capabilities for intragroup cooperation to deter cheating. Things like abilities in their brains for cheater detection, a "theory of mind", and ethical reasoning.

Other considerations suggest that worsening environmental conditions leads to more intergroup warfare (if population density is high enough, so that there is competition for resources, not merely strugle to survive, as on an island without competing groups). Such warfare would also promote cooperation and intragroup altruism over cheating.

What kind of cooperation is helpful in the non-warfare scenario? Sharing of resources (food, shelter, tools, clothing, etc.) Also communal support for raising orphaned children. Groups that had such customs and low proportions of cheaters would be more likely to survive at all.

Incidentally, one of the principal investigators (Chris Thompson) in the slime mold study, seems to know his subject pretty well. Here's another item about his slime mold research.