Yet another Symphony of Science

Posted on February 25, 2010 by Michael

This one includes some familiar and some new ‘singers’ (including someone without a penis for the first time in the series): Michael Shermer, Jacob Bronowski, Carl Sagan, Neil deGrasse Tyson, Richard Dawkins, Jill Tarter, Lawrence Krauss, Richard Feynman, Brian Greene, Stephen Hawking, Carolyn Porco, and PZ Myers.

(Whoops. As a commenter pointed out, Jane Goodall was in the last one. But this one has two women, so, uh, there.)

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A HUGE thank you to PZ

Posted on February 17, 2010 by Michael

I thought the big story of the day for me was the fact that my main blog, For the Sake of Science, was inappropriately shut down. As it turns out, there’s even bigger (and far better) news.

There’s another way you can tell [Christopher Maloney’s] a quack. When a student, Michael Hawkins, dared to criticize him, pointing out that “Naturopathic medicine is pure bull” and stating that naturopaths are underqualified and do not deserve the title of “doctor,” Maloney took action to silence him. After all, we can’t have people questioning quacks — that just makes them look even more ridiculous, which could lead to a loss of business.

So Maloney complained to WordPress, where Hawkins blog was located, and got them to shut it down. This does not speak well of craven WordPress; if you’re using WordPress hosting, you might want to reconsider it and move elsewhere. You know, to someplace that respects reality.

Now, given what has transpired so far with WordPress, I’m unfortunately timid. Believe me, once this blog moves to a more suitable location, words of loathing will fly. But until then, I feel horribly restricted. Therefore, it is probably necessary to point out that I am quoting someone. I did not just say those things about Christopher Maloney.

But really. This pinch on my free speech cannot stand for much longer.

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The placebo effect

Posted on February 10, 2010 by Michael

Hear that naturopaths? Lying is not ethical.

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Oh, How Times Have Changed

Posted on January 27, 2010 by Michael

By Michael Hawkins

In all my attempts to explain certain things about science, I’ve noticed something: a lot of people just don’t know the general timeline of significant events. These are important things to know, if only so one can at least have a general idea of what’s going on whenever science is discussed. Even more to the point, I would have to imagine a lot of people care where their money is spent. In Europe, for instance, one of the largest scientific collaborations amongst nations, the Large Hadron Collider, has a budget of roughly 9 billion dollars. Most of that is not American money, but regardless, the people who are paying for it ought to know that it is entirely predicated on the notion that the Universe emerged from the Big Bang roughly 13.7 billion years ago. If someone believes instead that the Universe is, say, 6,000 years old, then there is clearly an issue. The predication on which the Large Hadron Collider stands doesn’t make much sense for that person.

So it is with that in mind that I present my own attempt to knock down that sort of ignorance, or at least give a refresher. “BYA” stands for “billion years ago”, with the substitute “M” meaning “million”, and “T” standing in for “thousand”.

13.7 bya – Big Bang
13.0 bya – First galaxies form
10.0 bya – Milky Way forms
4.6 bya – The Sun forms
4.5 bya – Earth forms
3.9 bya – First life appears
3.0 bya – Photosynthesis appears
2.1 bya – Eukaryotic cells appear (you are a eukaryote)
1.0 bya – Multicellular life appears
580 mya – Cambrian explosion, tons of complex arms races evolve
400 mya – Tetrapods evolve
360 mya – Amphibians evolve
230 mya – Dinosaurs evolve
200 mya – Mammals evolve
150 mya – Birds evolve (we would have called them dinosaurs at the time)
65 mya – Big ol’ asteroid. Dinosaurs that can’t fly die out
50 mya – With T-Rex et al gone, mammals diversify
5-7 mya – Great apes, monkeys split (humans are great apes)
2.6 mya – Earliest tool use detected
150 tya – First anatomically apparent humans emerge
30 tya – Last Neanderthals die
15 tya – Wolves domesticated as dogs
11 tya – End of last ice age
5 tya – First preserved written language
3 tya – Egyptians build pyramids. Also praise cats.
476 AD – Fall of Rome
1643 – Newton is born
1743 – Thomas Jefferson is born
1809 – Charles Darwin and Abraham Lincoln are born (same day)
1999 – Mystery Science Theater 3000 is cancelled
2009 – See evening news

So there you have it. A basic sketch of what has happened over the past 13.7 billion years. While most events, such as the extinction of the dinosaurs 65 million years ago, don’t tend to be as hurtful as the cancellation of Mystery Science Theater 3000, they are all important.

Finally, the point of the time line I want to really take a moment to point out is with the evolution of humans. The split between us and other modern apes occurred roughly 5-7 million years ago. Emphasis on “other”. There is no taxonomic grouping that separates humans and, say, orangutans on the Family level. Humans, orangutans, gorillas, and chimpanzees are all Great Apes. Further included in that grouping would be a massive number of extinct species, many of which would resemble early humans in a number of ways. (And by “early”, I mean humans from just 50,000-100,000 years ago.) We are apes, which are first primates which are first mammals which are first vertebrates which are first animals which are first eukaryotes which are first simple replicators which are first the stuff of stars.

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Devil Facial Tumour Disease

Posted on January 27, 2010 by Michael

The seemingly needless “u” in “Tumour” is how it is written in reference to the disease, regardless of the country.

By Michael Hawkins

Devil Facial Tumour Disease is a particularly nasty cancer afflicting the Tasmanian devil population of Tasmania right now. It is spread by devils biting each other in the face and has been fatal for upwards of 50% of the population. Recent research has shed some light onto its origins.

Australian scientists found that the disease originates in Schwann cells, which protect peripheral nerve fibers. This has opened the door to the discovery of a genetic marker which can be used to diagnose the cancer.

What they also found was that in each subject, the disease was fundamentally the same. That is, the cancer does not originate in the individual devils, but instead comes from one common source, some long deceased devil. This means the disease can effectively be regarded as a separate organism, free to undergo its own evolution. Of course, its evolutionary ‘goals’ do not jive with the evolutionary ‘goals’ of its host, so there is an obvious conflict. (Please note the scare quotes around “goals”. The term is metaphorical.)

The cancer may become more and more virulent, allowing it to spread further and faster around the island. That could mean the end of both the devils and the cancer. Eventual death is not a very good long term evolutionary strategy, but then natural selection does not have any sort of foresight. Alternatively, the cancer could become less virulent so that its host could survive longer, thus offering the devil a greater chance to pass the disease along. Either way, the devils are out of luck.

One question this indirectly raises is if this susceptibility to cancer has anything to do with poor contact inhibition, the mechanism by which cells stop reproducing upon coming into contact with each other. Cells that don’t do that are called cancer. Most animals have one gene for this (p27), but naked mole rats have two (p27 and p16). This constitutes an extra barrier against cancer; as such, naked mole rats have never been observed to have developed cancer. Ever.

This means that at least one theoretical avenue of research into the cancer afflicting devils could be into the efficacy of their p27 gene: it may not offer the same effectiveness it does in other animals, especially considering the devil’s susceptibility to cancer in general.

But wherever the research should go, the dwindling Tasmanian devil population clearly needs help. And soon.

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Open your eyes

Posted on January 24, 2010 by Michael

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Greatest Scientific Events of the 20th Century

Posted on January 20, 2010 by Michael

I’ve recently been kicking around my personal list of what might constitute the greatest scientific achievements of the 20th century. There are so many things to consider and the list is necessarily so subjective that I’m not going to pretend to be giving a highly considered, thoroughly vetted list. I have put thought into this, but there will surely be dozens of examples I could easily find myself reconsidering if brought to my attention.

5) The Expanding Universe

In 1929 Edwin Hubble made the discovery that the Universe is actually expanding. This had direct implications throughout physics and astronomy. It was the reason Einstein called his cosmological constant “the biggest blunder” of his life.

Hubble used Cepheids, commonly known as “standard candles”, to get the relative distances of various galaxies. He then plotted this against their known redshifts. What he discovered was that these redshifts increased as a linear function of distance. That is, the Universe was uniformly expanding. In 1998 it would be discovered that this expansion was actually increasing in speed, contrary to expectations.

4) Cosmic Microwave Background Radiation

In the early 60’s, Robert Dickie was searching for the radiation that should have been left over if the Big Bang model was correct. He had assembled a team to look for what science had predicted, but he was beaten to the punch by Arno Penzias and Robert Wilson. And they weren’t even looking for the CMB.

Using a Dickie radiometer (designed by Dickie himself), Penzias and Wilson happened upon an interfering sort of fuzz while doing other research in 1965. They assumed it was coming from some nearby source, perhaps New York. After ruling out all the obvious possibilities (including pigeons), they were unable to conclude precisely what it was. They published a paper describing their results, which Dickie then used to correctly interpret as the discovery of the CMB. Penzias and Wilson won Nobel Prizes in 1978.

3) The Structure of DNA

There’s the saying that nothing in biology makes sense except in the light of evolution. This is crucially true, but the essence of the saying can be broaden to another area in biology: nothing in biology makes sense except in the light of the structure of DNA as discovered by James Watson and Francis Crick in 1953. I dare say, aside from Darwin’s discovery of how evolution happens, the discovery of the molecular shape of DNA has been the most significant event in all of biology. Interestingly, it shouldn’t have happened the way it did. Watson and Crick were one of several teams studying the structure. One member of another team, Rosalind Franklin, had actually produced accurate images of the molecule on her own, but determined she wasn’t ready to present her findings quite yet. Her teammate, Maurice Wilkins, would have none of that and decided to show her images – covertly – to Watson and Crick. They almost immediately recognized its significance (and to an extent Franklin hadn’t quite grasped): DNA formed as a double-helix with a uniform width all the way up its length.

Franklin’s work has unfortunately been drowned in history because of Wilkins’ betrayal, not to mention the fact that she is a woman in science – and that’s no easy task (especially in 1953).

Watson, Crick, and Wilkins received their Nobel Prizes in 1962 – Franklin got nothing.

2) General Theory of Relativity

Albert Einstein described his general theory of relativity in 1915, updating Newton’s ideas on gravity. He presented one of the most brilliant ideas man has ever had, fundamentally changing our understanding of how the Universe works. His science knocked down the notion of absolutes within spacetime, indeed, even helping to define the term. (Credit does not go directly to him, but his theory of special relativity was key in the development of the concept, and general relativity is an expansion of special relativity.)

Einstein received his Nobel Prize in 1922 (for 1921). (It was given for work as it specifically pertained to his special theory of relativity, not his theory of general relativity.)

1) Life on Mars

For the life of me, I don’t understand why no one seems to care about this. NASA recently announced it had reexamined a meteorite discovered in 1984 and confirmed that it contained within it microbial life which did not originate on Earth. While that may seem unfitting for a post about 20th century discoveries and events, the meteorite was originally described in 1996 to much fanfare. Over time a quiet consensus grew that the shapes in the rock could be formed via geological processes. The recent analysis blew those concerns out of the water.

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Negative thinking can go a long way

Posted on January 12, 2010 by Michael

Psychology is far from my primary interest in science, but I was fortunate enough to come by a story on negative thinking that I found highly interesting. There’s a lot of stuff out there that goes contrary to our intuition but ultimately makes logical sense.

Here’s how [John] Cloud explains the psychology of Hayes and like minds:

Hayes and other third wavers say trying to correct negative thoughts can, paradoxically, intensify them, in the same way that a dieter who keeps telling himself “I really don’t want the pizza” ends up obsessing about … pizza. Rather, Hayes and the roughly 12,000 students and professionals who have been trained in his formal psychotherapy, which is called acceptance and commitment therapy (ACT), say we should acknowledge that negative thoughts recur throughout life. Instead of challenging them, Hayes says, we should concentrate on identifying and committing to our values. Once we become willing to feel negative emotions, he argues, we will find it easier to figure out what life should be about and get on with it. That’s easier said than done, of course, but his point is that it’s hard to think about the big things when we’re trying so hard to regulate our thinking.

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It’s all about shape

Posted on January 11, 2010 by Michael

If there’s one phrase that has framed virtually all my education in biology the best, it would be “It’s all about shape.”

Probably the easiest way to think about this is with an analogy of a key and a keyhole. That’s how biological and chemical interactions occur – one thing fits into another. And so that’s the case with what researchers have done with the restoration of the activity of a particular enzyme.

The enzyme, called ALDH2, plays an important role in metabolizing alcohol and other toxins, including those created by a lack of oxygen in the wake of a heart attack. It also is involved in the metabolism of nitroglycerin, which is used to prevent chest pain (angina) caused by restricted blood flow and oxygen to the heart.

The problem is that a lot of people have a mutation in the gene which codes for this enzyme. This presents a couple of options. One is gene therapy where, in effect, a small piece of the genome (just a single gene) is altered, usually using an adeno-associated virus to introduce the correct DNA sequence into a nucleus (as happened with the spider monkeys recently cured of color blindness). This presents some problems because there isn’t a one-to-one correspondence with genes and proteins or enzymes. Alternative splicing means that a single gene can code for several different proteins. Sure, a correction may be just right for making one correct protein, but it may not also be correct for other proteins. This can result in serious side effects (though it didn’t in the spider monkeys). There are other reasons gene therapy can go awry, too, so it isn’t necessarily the best choice, however promising the field is for curing innumerable afflictions.

Then there’s the option these researchers took. Instead of messing around with anything to do with the genome, they looked at the proteome. Specifically, they looked at the enzyme ALDH2. Its mutated form doesn’t perform very well. It still works because it maintains some of its shape, but its active site does not comport to the appropriate substrates of the other molecules its trying to act upon as well as it should. So in effect, researchers took a compound (Alda-1) and injected into test subjects. In turn, this compound altered the shape of ALDH2, putting it back in proper working form.

“Because of the mutation in the gene, parts of the protein structure become loose and floppy. Alda-1 reactivates the enzyme by propping up those parts of the structure so they regain normal function,” said Dr. Hurley, director of the Center for Structural Biology on the Indiana University-Purdue University Indianapolis campus.

It’s an elegantly simple idea with a complex execution.

Incidentally, this all can be related to evolution in that if an enzyme has a given shape which catalyzes something even a little, it can be sculpted by natural selection to better catalyze that reaction, eventually getting to a relative optimum in shape.

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Symphony of Science, part 4

Posted on January 6, 2010 by Michael

Here’s the fourth autotuned work.

I was especially taken by the orangutan using a boat.

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