Open Thread

This should amuse fans of that Samuel Jackson movie that hasn’t come out yet.

A meta-study suggests that the health benefits of alcohol may be a statistical artifact. I still maintain that teetotalers don’t actually live longer, it just feels longer.

Chat about whatever.








Friday Beer Blogging – Flies Like Us

In my opinion hangover sufferers deny any memory of the night preceding (and therefore, apparently, limit their responsibility for whatever they did) more often that it’s actually true. The whole idea sounded like a myth to me, until one night in college…Anyhow, thanks to the work of UCSF researcher Ulrike Heberlein we now have some idea not only that I was wrong, but how the phenomenon might work. So here is a toast to some of the coolest research in recent years, the discovery of a set of alcohol-sensitive mutants named cheapdate, lightweight, barfly and tipsy, and what drunk flies have to say about us.

In my science posting I haven’t given fly geneticists that much credit because, to be honest, I’m unfairly biased against the fly guys. In fact half of what we know about genetics today we know because of the humble fruit fly Drosophila melanogaster. If genetics was American music fruit flies are folk, blues, jazz, R&B and half of rock and roll. Stretching the analogy further, human genetics came on temporally and influence-wise about like rap.

The simple reason for that is similar to why practically everybody in the early days of biochemistry found himself or herself studying hemoglobin. Basically, unlike most proteins hemoglobin has a color (red). That means that people who wanted to purify hemoglobin from all of the other proteins in the body didn’t need a UV spectrometer or any other fancy gimmick that we developed later. They could just run mashed-up tissue through a series of purification columns based on the protein’s size, charge and affinity for hydrophobic vs. hydrophilic surfaces (oil vs. water), and collect just the red stuff. After a series of those, voila, you end up with pure hemoglobin. I’ve actually done that and while I would not call it easy, compared with the hoops people go through to purify practically any other protein getting pure hemoglobin is a stone cinch.

Fruit flies (cute picture of Drosophila at left) have unique salivary glands which produce hundreds of copies of each chromosome rather than the usual two. In cells preparing to divide these mega-chromosomes condense and line up next to each other, as seen on right:

fig 1
A: Meet Drosophila melanogaster. Image: c J.Berger, Max-Planck-
Institute Tübingen; B: The Drosophila chromosome squash, God’s gift to genetics.

It turned out that drosophila chromosomes (there are four, plus a sex chromosome) have characterstic banding patterns that correspond to intervals of dense and less-dense DNA. In short order folks mapped the light-and-dark bands on every chromosome, and then the big leap happened as far as genetics is concerned. Some fruit flies carried a mutation, say curled-up wings or odd-colored eyes, which seemed to pass on to the next generation along with a slight disturbance in their chromosome banding. One specific band was gone, or it appeared twice, or a series of bands had been cut out and put back in reverse.

Eventually people mapped hundreds of mutants to their respective defects on the chromosome. Now let’s say that you want to map genes that makes wings become wings instead of a new pair of legs. Using the existing ‘map’ of known mutations pinpointing the location of a new mutation becomes no problem. Just breed your unknown mutant with known, already-mapped mutants. If the mystery mutant and the known mutant sit on different chromosomes or a long way from each other on the same chromosome the grandkids of your ‘testcross’ will have an even mix of either one of the mutations, both or neither. If the genes fall close to eath other, however, you find that most of the grandkids have both mutations or neither and very few with one or the other.

These simple tools, plus a few that I’ve left out, allowed the fly-pushers to uncover the fundamental rules of genetics. A large fraction of known human genes first made their appearance when somebody discovered a fruit fly with a unique characterstic, mapped the mutant and discovered what the gene does. Since they can’t perform very many ethical experiments on their subjects, human geneticists often start off with the fruits of a fly pusher’s work and simply look to see whether the same or similar gene can be found in us. I’m necessarily giving short shrift to the great folks working in yeast genetics, but this being a beer blog the topic of yeast hardly gets ignored.

By now it should be clear why a young scientist who wanted to uncover the basic genetics of inebriation, alcoholism and alcohol tolerance chose to work with fruit flies. There’s a bit more – on top of fruit flies being a great genetic model, people and flies both have a history of alcohol consumption that stretches back over evolutionary time (read more about that here) and we have nervous systems that largely work in the same way, so there’s reason to expect that we and they will respond similarly. As Heberlein noted recently:

It became immediately apparent that the behavioral changes elicited by acute ethanol exposure are remarkably similar in flies and mammals. Flies show signs of acute intoxication, which range from locomotor stimulation at low doses to complete sedation at higher doses and they develop tolerance upon intermittent ethanol exposure. [Heberlein et al. (2004) Integrative and Comparative Biology 44:269-274]

You cannot tell fly researchers apart based on how they make mutations – there are only a few more-or-less standard ways to insert random mistakes into a fly’s genome – and once one identifies a mutation the procedures for tracking down where exactly the mistake happened are more or less standard. The real magic is in the behavioral assays that fly-pushers come up with to select mutations they want out of thousands and thousands of randomly-mutated flies. Folks searching for the genes controlling flight will look for flies that can’t reach an elevated food trap while folks asking which genes control memory will test to see which flies can’t learn to choose only the food that does not carry a mild electric charge. In a search for mutants that got drunk unusually fast Heberlein built the inebriometer.

Fig 2
A – the alcohol without liquid (AWOL) inhaler; B – Dr. Heberlein’s
inebriometer*. Copyright Cell Press

Heberlein’s device (B) basically amounts to an alcohol vaporizer (A) connected to a column of funnels stacked on top of each other. Flies start out in the space at the top of the column, but as the effects of demon rum set in they lose their coordination and drop into the next column, and then the one after that, and so on. Eventually the drunkest flies reach the pass-out stage and drop through straight to the bottom.

The first fly to drop out of Heberlein’s inebriometer, the appropriately-named cheapdate mutant, barely needed the fly equivalent of a Kahlua shot before it folded it up its wings and dropped. Cheapdate unexpectedly mapped to a protein called amnesiac, so named because amnesiac mutant flies show a total block in tests for learning and memory. More mutants originally known for their defects in memory and learning – rutabaga and fasciclin II – went throught the inebriometer and dropped out almost as fast as cheapdate. These results suggest that the same proteins which keep our gin-soaked brains operating are actually moonlighting from their regular job as mediators of memory.

The amnesiac gene encodes a neurotransmitter while rutabaga makes a protein involved in the cyclic-AMP signaling pathway. More mutants have been identified but haven’t yet been characterized to the same degree as cheapdate: lightweight has the same effect as cheapdate but acts on a different gene, while barfly and tipsy have opposite effects in the inebriometer, the former making flies more resistant to alcohol and the latter making them sensitive. Unlike cheapdate and lightweight, barfly and tipsy influence alcohol’s sedative effect instead of its impact on posture and coordination.

Like any good research the work by Dr. Heberlein and others raises ten questions before it gets close to answering one. Does a drinking binge swamp the cAMP signaling pathway so badly keeping our soaked brains functioning that it can’t keep up with its usual job of making memory? Could be. Dr. Heberlein has already made the leap from flies to mammals, so we may know much more soon.

(*) Bellen, C. (1998) Cell 93: 909-912



Changes to Corporate Accounting

At first glance, I would say this is long overdue:

The board that writes accounting rules for American business is proposing a new method of reporting pension obligations that is likely to show that many companies have a lot more debt than was obvious before.

In some cases, particularly at old industrial companies like automakers, the newly disclosed obligations are likely to be so large that they will wipe out the net worth of the company.

The panel, the Financial Accounting Standards Board, said the new method, which it plans to issue today for public comment, would address a widespread complaint about the current pension accounting method: that it exposes shareholders and employees to billions of dollars in risks that they cannot easily see or evaluate. The new accounting rule would also apply to retirees’ health plans and other benefits.

A member of the accounting board, George Batavick, said, “We took on this project because the current accounting standards just don’t provide complete information about these obligations.”

***

Using information in the footnotes of Ford’s 2005 financial statements, Ms. Pegg said that if the new rule were already in effect, Ford’s balance sheet would reflect about $20 billion more in obligations than it now does. The full recognition of health care promised to Ford’s retirees accounts for most of the difference. Ford now reports a net worth of $14 billion. That would be wiped out under the new rule. Ford officials said they had not evaluated the effect of the new accounting rule and therefore could not comment.

Applying the same method to General Motors’ balance sheet suggests that if the accounting rule had been in effect at the end of 2005, there would be a swing of about $37 billion. At the end of 2005, the company reported a net worth of $14.6 billion. A G.M. spokesman declined to comment, noting that the new accounting rule had not yet been issued.

I don;t know how this would impact the overall stock market in the short run, but it appears that in the long run this would be a change towards more healthy accounting practices. You business folks can correct me if I am wrong.








The Power of Prayer

This is timely, considering my objection to Gov. Manchin’s remarks yesterday:

Prayers offered by strangers had no effect on the recovery of people who were undergoing heart surgery, a large and long-awaited study has found.

And patients who knew they were being prayed for had a higher rate of post-operative complications like abnormal heart rhythms, perhaps because of the expectations the prayers created, the researchers suggested.

Because it is the most scientifically rigorous investigation of whether prayer can heal illness, the study, begun almost a decade ago and involving more than 1,800 patients, has for years been the subject of speculation.

The question has been a contentious one among researchers. Proponents have argued that prayer is perhaps the most deeply human response to disease, and that it may relieve suffering by some mechanism that is not yet understood. Skeptics have contended that studying prayer is a waste of money and that it presupposes supernatural intervention, putting it by definition beyond the reach of science.

I am a little surprised that the results were negative, because if you had asked me beforehand, I would have told you they would find nothing at all- no statistically significant relationships whatsoever. I have no idea how large the relationships were, how they controlled for things, etc., but I would bet it was rigorously done given how contentious there findings were going to be.

At any rate, the one thing the study did not apparently look at was who prayer is really designed for- the people praying, not the target of the prayers. When those miners were stuck in the mine in Sago, no amount of prayer was going to help them get out. Prayer did, on the other hand, really help the families of the victims. It gave them something to do and it gave them a sense that they were doing somthing to help, as well as bringing the group together in a shared activity when they needed suuport the most. So, regardless what this study shows, I wouldn’t say prayer is useless, because prayer is helping someone in these circumstances.








Gay Marriage Ruling

There has been a gay marriage ruling in Mass.:

Massachusetts’s highest court ruled today that same-sex couples who live in other states cannot get married in Massachusetts unless gay marriage is legal in their home states.

In an opinion written by Justice Francis X. Spina, the court upheld a 1913 statute that says that no out-of-state resident can get married in Massachusetts if the marriage would be void in the person’s home state, unless the person intends to live in Massachusetts. Five justices concurred, at least in part, with Justice Spina’s opinion; one justice dissented.

“The laws of this commonwealth have not endowed nonresidents with an unfettered right to marry,” Justice Spina wrote for the majority. “To the contrary, the rights of nonresidents to marry in Massachusetts have been specifically restricted.”

He added, “I recognize that the brunt” of the law’s impact “has inevitably fallen disproportionately on nonresident same-sex couples rather than on nonresident opposite-sex couples” because no other state currently allows gay marriage.

I do not know about the legal reasoning in this ruling, but this seems reasonable to me.








Miner Released

This is rather extraordinary:

Sago Mine survivor Randal McCloy Jr., looking thin and stiff but walking on his own, offered his gratitude Thursday as he was released from a hospital after almost three months.

”I’d just like to thank everybody for their thoughts and prayers” McCloy said softly, wearing a ball cap and a racing-team jacket at a morning news conference. He paused, then added with a weak smile, ”I believe that’s it.”

His doctors say they can’t explain why McCloy, who was trapped underground for more than 40 hours after the Jan. 2 mine explosion, survived the carbon monoxide exposure while all 12 other miners with him died. Medical crews at the mine and the doctors who first treated him have said McCloy, too, was close to death.

I listened to the press conference this morning while riding the bus to work, and it really is amazing how quickly he has recovered, especially considering he was unresponsive until Valentine’s Day. Governor Manchin, who I normally like a great deal, irritated me a little bit when he claimed the recovery was ‘proof of a higher power’ (which made me wonder why the higher power killed the other 12), but this extraordinary and a good day for McCloy and his family.








I Beg You

I can take the harangues directed at me. I can take the intentional and unintentional misreading of what I write. I can take the flaming.

Why?

Because as far as I am concerned, I give as good as I get.

What I can not take, however, is some of you refusing to embed your links in the comments. I am speaking to you, Richard Bottoms (as well as many others). I am calling you out. Use the damned link function and start embedding your links, or fear my wrath. Or something.

*** UPDATE ***

I should probably point out why this infuriates me- because when you do not do it, and just insert a link that is super long, you break the layout of the page and screw up the margins. Then I have to go and edit it or delete your comment (which is what I am going to start doing, rather than fixing them as I have in the past).

*** Update ***

And stop posting entire stories in the comments (Slide- this one is aimed at you). It is especially irritating when you do that and don’t even provide a link. If you provide the damned link (and embed it like a good commenter), miracle of miracles, people will click on it and read the story.

Fascinating stuff.