Bacteria that Commit Honourable Suicide

How can any samurai, kosher or otherwise, NOT be attracted by this title?

The Bacteria that Commit Honourable Suicide

Bio-cell seppuku. Kamikaze microbes. Organically pre-programmed harikiri. You got to love it.

OK, kids, it goes something like this…

In multicellular organisms (like us) it is essential that every cell behaves and does the job it was produced to perform. The survival of a multicellular organism depends on this – every cell in our bodird is tightly controlled in terms of how big it can grow (fairly big), when it can reproduce (almost never) and what sort of metabolic processes it may carry out. And, like a dystopian sci-fi future, any cell that steps out of line is put to death.

Not by surrounding cells… but by its own internal processes!!

Each cell in the human body is programmed to die. Death is their default state. It is only by behaving, by obeying outside orders and carrying out the processes it’s meant to, that the cell is able to inhibit its own destruction. This is a good thing for the body as a whole, because cells that do manage to escape the tight death-regulation control are cancerous cells, and cause havoc within the body.

This makes sense for cells within a multicellular organism who, after all, have an entire body to maintain. What is less certain is why bacteria would want to have death pathways within their cells. Because strangely enough they do! [1]

Although the mechanism for self-destruction is very interesting [2], it still leaves the big unanswered question of why the bacteria do this. What possible reason would there by for a unicellular organism to kill itself? One observation that might help to answer is that there is a quorum-sensing molecule that is produced by surrounding bacteria of the same species. This suggests a high degree of colony behaviour from the bacteria… the reason one cell dies is because the colony cannot cope with having a crazy rogue cell anymore than the inside of a human body can.

Talk about peer pressure!

But if both pathways lead ultimately to death, what is the point of choosing between them? One suggestion is that if there are lots of bacteria around in a colony, it makes more sense to kill off any that start to go genetically screwy. If there are many bacteria around, then any cell with small amounts of DNA damage will discreetly commit suicide.

DNA may be ‘selfish’, but the emergent behaviour of cells can get pretty altruistic at times!

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[1] In E. coli two genes, called mazE and mazF are encoded on the same bit of DNA (the same operon). MazF encodes a killer toxin, while mazE makes the antitoxin. If the mazE DNA is damaged, or the mazE protein made by the DNA is inhibited, then the mazF will be let loose and the cell will die.

[2] In the case of large amounts of DNA damage, the DNA repair system is mediated by a protein called RecA. A rise in the amount of messenger RNA for RecA (messenger RNA is used to make the protein from the DNA) triggers cell death in E. coli by causing the cell membrane to depolarise, breaking down cellular integrity and leading to cell death. When the mazEF system is activated it will inhibit RecA; in cells where the mazEF system has been removed higher levels of mRNA Rec A were found. And cells with both RecA and the mazEF systems removed were much less likely to die. Cells with both of the death-pathways removed were surviving longer despite damage to the DNA.

(A simple diagram of the interactions between the two)

About the Author: A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs. Follow on Twitter @labratting.

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Exhibit Two Gets Aished!

(Exhibit Two at Aish HaTorah in Jerusalem earlier this month)

A bit of explanation is in order.

Aish = Aish HaTorah. [1]

Aish HaTorah is an apolitical network of Jewish educational centers in 35 branches on five continents. [2]

Aish is all about Jewish education and kiruv… drawing Jews closer to G-d. [3]

There is an expression for Jews who, through the educational and kiruv work of Aish HaTorah, become more connected to Judaism and more observant. It is said they get “Aished.”

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[1] The name Aish HaTorah literally means “Fire of Torah.” As Elie Weisel said: “Aish HaTorah means to me the passion of teaching, the passion of learning. The study of Torah, the source of Jewish values, is the way to Jewish survival.”

[2] Aish HaTorah is a Jewish outreach organization started in Jerusalem by Rabbi Noah Weinberg z”l in 1974. Aish HaTorah’s goal is to revitalize the Jewish people by providing opportunities for Jews of all backgrounds to discover their heritage in an atmosphere of open inquiry and mutual respect. Aish HaTorah is regarded as a world leader in creative Jewish educational programs and leadership training.

[3] Aish’s educational philosophy is that Judaism is not all or nothing; it is a journey where every step counts, to be pursued according to one’s own pace and interest. Mitzvot (commandments) are not rituals, but opportunities for personal growth, to be studied and understood. We learn the Torah’s wisdom to enrich our own lives, and to share these ideas with all humanity.

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Loonies I Have Lunched With (Part 6): Creamer Eyes

You may have seen them out of the corner of your eye… at the next table or across the restaurant.

Sometimes, you may have had the misfortune of seeing them up close and personal, across the table from you.

No matter how you run into them or how they are inflicted upon you… the result is usually the same. Stunned disbelief.

My beloved friend, CW, and I were sitting down to dinner… minding our own business. Conversation, as always, was sparkling and witty. ‘Gay banter’ some may have called it a more innocent by-gone era.

She looked up, starting to make a point. She froze in mid-sentence. I can only imagine the look on her face. And I say that literally since I was unable to see her. Why?

Well, I think the answer by now is obvious.

I smiled and casually asked, “What?”

I removed my impromptu eye-wear and gazed at my dearly beloved friend, her eyes closed, shaking her head.

I had achieved the desired reaction.

I think what really did the trick was the fact that I had added two dark blue ‘pupils’ on the bottom of the creamers.

Not unlike The Spanish Inquisition, nobody expects the Creamer Eyes.

And yet, when one is confronted with them, there is a sense of inevitability about the encounter.

“It was just a matter of time, I suppose,” seems to be the over-riding sense.

Resignation to the inevitability of the Creamer Eyes. A sense of defeat… of being bested by the childishness of it all.

And yet, you cannot help but stifle a giggle as you shake your head in disbelief.

So, here’s to Creamer Eyes… and to the loonies who don them!

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Dogs may have helped Humans beat the Neanderthals

Dogs may have helped Humans beat the Neanderthals

One of the most compelling – and enduring – mysteries in archaeology concerns the rise of early humans and the decline of Neanderthals. For about 250,000 years, Neanderthals lived and evolved, quite successfully, in the area that is now Europe. Somewhere between 45,000 and 35,000 years ago, early humans came along.

They proliferated in their new environment, their population increasing tenfold in the 10,000 years after they arrived; Neanderthals declined and finally died away.(The skull of what may be the earliest known dog, which dates to 31,700 years ago. The prehistoric skull was excavated at Goyet Cave in Belgium.)

What happened? What went so wrong for the Neanderthals — and what went so right for us humans?

The cause, some theories go, may have been environmental, with Neanderthals’ decline a byproduct of – yikes – climate change. It may have been social as humans developed the ability to cooperate and avail themselves of the evolutionary benefits of social cohesion. It may have been technological, with humans simply developing more advanced tools and hunting weapons that allowed them to snare food while their less-skilled counterparts starved away.

The Cambridge researchers Paul Mellars and Jennifer French have another theory, though. In a paper in the journal Science, they concluded that “numerical supremacy alone may have been a critical factor” in human dominance – with humans simply crowding out the Neanderthals. Now, with an analysis in American Scientist, the anthropologist Pat Shipman is building on their work. After analyzing the Mellars and French paper and comparing it with the extant literature, Shipman has come to an intriguing conclusion: that humans’ comparative evolutionary fitness owes itself to the domestication of… dogs.

Yep. Man’s best friend, Shipman suggests, might also be humanity’s best friend. Dogs might have been the technology that allowed early humans to flourish.

Shipman analyzed the results of excavations of fossilized canid bones – from Europe, during the time when humans and Neanderthals overlapped. Put together, they furnish some compelling evidence that early humans, first of all, engaged in ritualistic dog worship. Canid skeletons found at a 27,000-year-old site in Předmostí, of the Czech Republic, displayed the poses of early ritual burial. Drill marks in canid teeth found at the same site suggest that early humans used those teeth as jewelry — and Paleolithic people, Shipman notes, rarely made adornments out of animals they simply used for food.

There’s also the more outlying fact that, like humans, dogs are rarely depicted in cave art – a suggestion that cave painters might have regarded dogs not as the game animals they tended to depict, but as fellow-travelers.

(Neanderthal man)

Shipman speculates that the affinity between humans and dogs manifested itself mainly in the way that it would go on to do for many more thousands of years: in the hunt. Dogs would help humans to identify their prey; but they would also work, the theory goes, as beasts of burden – playing the same role for early humans as they played for the Blackfeet and Hidatsa of the American West, who bred large, strong dogs specifically for hauling strapped-on packs. (Paleolithic dogs were big to begin with: They had, their skeletons suggest, a body mass of at least 70 pounds and a shoulder height of at least 2 feet – which would make them, at minimum, the size of a modern-day German Shepherd.) Since transporting animal carcasses is an energy-intensive task, getting dogs to do that work would mean that humans could concentrate their energy on more productive endeavors: hunting, gathering, reproducing.

The possible result, Shipman argues, was a virtuous circle of cooperation — one in which humans and their canine friends got stronger, together, over time.

There’s another intriguing — if conjecture-filled — theory here, too. It could be, Shipman suggests, that dogs represented even more than companionate technologies to Paleolithic man. It could be that their cooperative proximity brought about its own effects on human evolution — in the same way that the domestication of cattle led to humans developing the ability to digest milk. Shipman points to the “cooperative eye hypothesis,” which builds on the observation that, compared to other primates, humans have highly visible sclerae (whites of the eyes). For purposes of lone hunting, sclerae represent a clear disadvantage: not only will your pesky eye-whites tend to stand out against a dark backdrop of a forest or rock, giving away your location, but they also reveal the direction of your gaze. It’s hard to be a stealthy hunter when your eyes are constantly taking away your stealth.

(Ancient dog – expressive eyes and the cooperative eye hypothesis)

Expressive eyes, however, for all their competitive disadvantage, have one big thing going for them: They’re great at communicating. With early humans hunting in groups, “cooperative eyes” may have allowed them to “talk” with each other, silently and therefore effectively: windows to the soul that are also evolutionarily advantageous. And that, in turn, might have led to a more ingrained impulse toward cooperation. Human babies, studies have shown, will automatically follow a gaze once a connection is made. Eye contact is second nature to us; but it’s a trait that makes us unique among our fellow primates.

Dogs, however, also recognize the power of the gaze. In a study conducted at Central European University, Shipman notes, “dogs performed as well as human infants at following the gaze of a speaker in tests in which the speaker’s head is held still.” Humans and their best friends share an affinity for eye contact — and we are fairly unique in that affinity. There’s a chance, Shipman says — though there’s much more work to be done before that chance can be converted even into a hypothesis — that we evolved that affinity together.

“No genetic study has yet confirmed the prevalence or absence of white sclerae in Paleolithic modern humans or in Neanderthals,” Shipman notes. “But if the white sclera mutation occurred more often among the former — perhaps by chance — this feature could have enhanced human-dog communication and promoted domestication.”

Which is another way of saying that, to the extent dogs were an evolutionary technology, they may have been a technology that changed us for the better. The old truism — we shape our tools, and afterward our tools shape us — may be as old, and as true, as humanity itself.

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Author: Megan Garber | Source: The Atlantic [May 14, 2012]

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One Year Anniversary!

One year ago, yesterday, May 17, 2011, I created this blog, the Kosher Samurai.

One year ago, today, I published my first blog article, set out below.

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I prefer to spell it bl*g or bl*gging.

I have some strange aversion to the way the word is usually spelled. Not sure why. I just do.

I’m sure that, in time, I will succumb and use the full un-asterixed version. But for now, this is my bl*g.

I’ve been inspired (or provoked, depending on one’s point of view) to start up this site by a dear friend of mine.

Shameless plug for dear friend of mine:  XUP

Her writing is quite good. If you haven’t done so already, check it out. Quality stuff, I assure you.

A few details about yours truly…

I’m Jewish and I have a fondness for Japan, Japanese food and Japanese culture.

(Hence the name for this site:  Kosher Samurai)

I am a criminal defence lawyer. Divorced

Two kids:

Exhibit One: 21 yr old daughter

Exhibit Two: 19 yr old son.

That’s all for now, I think. I’m new to this so I need to get past my “green as Gumby” stage and start writing.

Bye for now

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Since then, I’ve published 162 blog articles, including this one.

At the Kosher Samurai, I publish three articles a week, usually posted on Mondays, Wednesdays and Fridays.

At my sister blog, Vampyre Fangs, I also publish three articles a week, usually posted on Mondays, Wednesdays and Fridays.

I want to personally thank each and every one of my readers who’ve stopped by and read my articles.

For me, it is a labour of love. I write primarily for myself but if others enjoy my writings too… that brings me great pleasure.

Thank you. And keep coming.

Sincerely,

The Kosher Samurai

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Are We Attracted To Our Opposite?

They say that opposites attract. That presumes that the attraction is mutual, I suppose.

(The gun totin’ Southern Redneck Good Ole Girl)

I’m not sure that is always, or even often, the case.

(Hitler Youth – more my son’s type than mine, really… but still…)

Take the example some of the kinds of women to whom I am attracted. [1] Now, I am not saying these are the types of women with whom I’ve ever been involved. I just feel drawn to them in some odd way.

(Goth beauty in black lace)

All are fantasies in one way or another. Figments of my imagination, as it were. Just the kind to which I feel a genuine, if somewhat confusing, attraction.

(Vampyre brides)

They are generally strong, somewhat dangerous women who know who they are and are at peace with that. Even comfortable with it.

(Warrior – Ancient)

If that is who they are, what does that say about what I think of myself? A disturbing thought. Are we attracted to characteristics that we lack… or to those we simply admire or value, whether we have them ourselves or not? Are we drawn to those who openly display traits that we choose to keep hidden?

(Warrior -Medieval)

This is not to say I am not also attracted to women who are ‘appropriate’… of course I am. But maybe it is the very inappropriateness of these ‘other types’ that forms part of the attraction. The whole ‘forbidden fruit’ thing. But even the forbidden fruit allusion implies that you can eat of it, if you choose, even though you know you mustn’t.

(Warrior – mix of new and old)

Conspicuously absent from this list are the types you might expect to see. Hollywood glamour types or blonde bombshells or scantily clad floozies with major league yabbahoes, to steal an expression from the movie Animal House. Aside from an initial ‘wow’ response when I first see them, there is no attraction for me. In fact, as a general rule (and as can be seen from the above sampling), I don’t really hold by what most people find ‘beautiful’ or even ‘attractive.’

(Warrior – Modern)

Hmmm… I just noticed that all but one of the women are ‘armed’ in one way or another [2] and that the last three ‘warrior women’ also happen to be vampyres! Bit of a cross-over of types there but… as I said… it can be confusing.

Luckily for me, I’m not the kind of person who revels in pop psychology. It’s a curious thing being drawn to these types of  women and while I don’t mind pointing this little quirk out, I’m not going to be spending an awful lot of thought on it.

 We all have our little idiosyncrasies.  This is one of mine.

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[1] I take it as a given that none of these types would even acknowledge that I am of the same species as they.

[2] The Goth Girl may give off the air of having a dark side, so the potential for harm is there… but not openly so. The others have weapons or, in the case of the Vampyre Brides, fangs and preternatural powers.

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Total Societal Meltdown: Not as Fun as You Might Think

Do you ever get the impression that there are people out there who just can’t wait for the world to go to hell in a handcart?

Whether it is a complete socio-economic meltdown, a total financial collapse, a global political conflagration or a good old-fashioned 3rd World War… do you get the feeling that there are those who will secretly say, “Yes! I was hoping for this!”

When I look at the Doomsday types… religious or otherwise… I can’t help but think that despite their dire warnings, deep down, they’re dying for the end to be near.

As you all probably know, I personally believe that if there is going to be a non-biblical end to Civilization As We Know It, it will be in the form of either a Zombie Apocalypse, a Robot Uprising or a Space Alien Invasion. All excellent and probable scenarios, of course.

(No matter how you slice it, it’s not so good for us)

But, believe it or not, there are others who feel that the world will experience The Big Collapse in other ways. Nuclear War is a popular one. A 99.9% effective disease ranks high in many people’s minds.

However we get there, I am sure a good many people will agree that what remains of mankind ends up eating stray dogs and fighting for the bones. Not an attractive idea but… as I said… I believe there are a good portion of people to whom this Mad Max dream world is heaven on earth.

I think these poor saps have a kind of Hollywood-induced image that makes post-civilized life somewhat bleakly romantic in a kind of modern Dark Ages way.

I’m not sure what you guys think, but from what I know about Europe between the Fall of Rome and early medieval times, I wouldn’t wish that life on my worst enemy. OK, maybe my worst enemy but that’s about it.

I see no romance in a life of grinding poverty, cruelty, ignorance and pestilence interrupted occasionally by the odd barbarian horde pillaging and raping everything in sight. And if you think you’ve witnessed religious fundamentalists in our day, trust me… you ain’t seen nothing compared to the way things were 1500 years ago.

And its not like you could ignore a disruption of that kind.

The only people I can imagine not noticing all that much that the world has fallen apart are those whose situation is already so bleak and desperate, it couldn’t get worse. People living out in the African, Australian, Southeast Asian or South American jungles or hinterlands with no contact with society already. If things headed south for the rest of us, how would they know… or even care?

Nope. Things going down the toilet is all well and good when we’re discussing The Upcoming Zombie Apocalypse and while it is a good idea to have a good survival plan in place in case of some natural disaster or toxic spill or the like, I don’t lay awake at night hoping and praying that things hit the fan on that massive a scale.

I’ll leave that to the survivalists in North Dakota or Montana or wherever the heck they hang out.

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Unhealthy Interests (Part 1): Zombies

I have been accused by more than one alleged friend of having an ‘Unhealthy Interest’ in zombies.

Well, honestly. These days, who doesn’t? I mean, really.

(♥ I’m a zombie girl… in a zombie world ♥)

Yes, but [1]… these so-called friends are quick to point out that, unlike yours truly, most other (i.e. normal) people…

• Are not lifetime members of The Zombie Research Society (with membership card in wallet to prove it);
• Haven’t given newspaper interviews or had newspaper articles written about them and zombies;
• Haven’t given lectures/seminars on the subject on zombies;
• Aren’t writing an ongoing Twitter fiction ‘journal-style’ story about life in The Upcoming Zombie Apocalypse;
• Don’t regularly write blog articles about zombies and The Upcoming Zombie Apocalypse;
• Don’t regularly use the expression ‘The Upcoming Zombie Apocalypse’;
• Don’t refer to Walmart as ‘The Zombie Serengeti’;
• Don’t have a large cache of weapons [2] in easy reach of their computer desks;
• Don’t have a 3-month supply of food in the basement; [3]
• Don’t have a dozen gallons of fresh water and boxes of Twinkies and Strawberry Pop-Tarts [4] in their apartments;
• Don’t call Twinkies and Strawberry Pop-Tarts ‘The Official Snacks of The Upcoming Zombie Apocalypse’; [5]
• Can’t speak for an hour straight on the most efficient/effective and least efficient/effective ways to kill zombies;

(The last thing a Georgia zombie sees)

The list goes on, as you can imagine.

Frankly, I don’t see how this interest of mine can be seen in any way as ‘unhealthy.’ If anything, it promotes emergency preparedness which, if done right, ensures survival.

(Yeah… I wish!)

And you can’t get much healthier than ‘not being eaten by hordes of living dead.’

So, back-off, buzz-kills!

You don’t see me kvetching about your ‘unhealthy interest’ in taking long walks and hitting little balls with sticks while wearing stupid gaily-colored pants.

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[1] “You know, my brother once told me that nothing someone says before the word ‘but’ really counts.” (Benjen Stark, ‘Game of Thrones’)

[2] Off the top of my head (and looking around me):  samurai blades, four (2 katanas, 1 wakizashi, 1 tanto); standard machete, one; bayonets, two (1 U.S. Indian wars, 1 French, WW1); Bowie knife, one;  gurka knife, one; ‘Book of Eli’ machete, two (1 large, 1 small); ‘Eragon’ medieval dagger (Arya’s blade), one; billhook sickle/machete, one.

[3] With respect, that’s my mother, not me. I barely have a 6-week supply. Hardly anything, really.

[4] Twinkies and Strawberry Pop-Tarts are the official snacks of The Upcoming Zombie Apocalypse.

[5] D’OH! 

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Gaseous Emissions from Dinosaurs May Have Warmed Prehistoric Earth

Dino Farts Contributed to Mesozoic Global Warming?

That’s the thought that flitted through my mind when I saw the headline…

As a Vampyre Fangs blog article disclosed a short time ago, this staggering information comes hot on the heels of another theory implicating (albeit with the help of VF’s fervent imagination and conspiracy theories) polar bear farts as a source of increased arctic methane emissions! [1]

What’s with the geeks and nerdlings over at ScienceDaily.com these days? For some odd reason,  the subject of passing gas seem to be hanging in the air (no pun intended) in the hallowed halls of that bastion of scientific research. Why the obsession with butt burps? Why the fixation on flatulence?

But I digress…

According to the article, “Sauropod dinosaurs could in principle have produced enough of the greenhouse gas methane to warm the climate many millions of years ago, at a time when Earth was warm and wet. That’s according to calculations reported in the May 8th issue of Current Biology, a Cell Press publication.”

“The hulking sauropods, distinctive for their enormous size and unusually long necks, were widespread about 150 million years ago. As in cows, methane-producing microbes aided the sauropods’ digestion by fermenting their plant food.”

So this was more than Bessy the Heifer and her pals floating the occasional air biscuit. We’re talking about huge herds of  herbivorous dinosaurs cutting the cheese on a breath-taking scale.

“A simple mathematical model suggests that the microbes living in sauropod dinosaurs may have produced enough methane to have an important effect on the Mesozoic climate,” said Dave Wilkinson of Liverpool John Moores University.”

OK, so sauropods shooting the canon en masse was problematic way back when. Now, how do their ancient anal salutes compare with modern stinky output?

“Indeed,” says Wilkinson, “our calculations suggest that these dinosaurs could have produced more methane than all modern sources – both natural and man-made – put together.”

Wilkinson and study coauthor Graeme Ruxton from the University of St Andrews were studying sauropod ecology when a question dawned on them: If modern cows produce enough methane gas to be of interest to climate scientists, what about sauropods?

What, indeed! Holsteins the size of small buildings blowing the big brown horn day in and day out. Whose imagination would not be fired up at the prospect?

They teamed up with methane expert Euan Nisbet at the University of London to work out the numbers.

Wilkinson confessed that “trying to estimate this for animals that are unlike anything living has to be a bit of an educated guess.” That did not stop the intrepid scientists from estimating the prehistoric poots.

Using estimated size and population densities [2], Wilkinson, Ruxton, and Nisbet calculate global methane emissions from sauropods to have been 520 million tons (520 Tg) per year, comparable to total modern methane emissions. Before industry took off on modern Earth about 150 years ago, methane emissions were roughly 200 Tg per year. By comparison, modern ruminant animals, including cows, goats, giraffes, and others, produce methane emission of 50 to 100 Tg per year.

[(1): Pull my finger! ~ (2): No way, dude!]

520 million tons per year! A serious pantload, by anyone’s calculations!

The study’s conclusions not only show “just how strange and wonderful the workings of the planet are” but also serve as a useful reminder for the importance of microbes and methane for global climate, the researchers say.

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[1] Not really true. I just can’t resist spreading this totally unfounded rumour. 

[2] A medium-sized sauropod weighed something like 20,000 kilograms (about 44,500 pounds – over 22 tons!) , and sauropods lived in densities ranging from a few large adults to a few tens of individuals per square kilometer.

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Sullivan Ballou Letter – Ashoken Farewell

I’ve not yet had the opportunity to see Ken Burns’ masterful work, The Civil War.

But I did see this one clip. [1]

A week before the Battle of Bull Run, Sullivan Ballou, a Major in the 2nd Rhode Island Volunteers, wrote home to his wife, Sarah, in Smithfield. The letter was written from Washington, D.C. July 14, 1861, on the eve of his unit moving out to war.

He wrote the letter in anticipation of his death.

It is, to me, the most moving love letter I’ve ever read. By the end, I was reduced to tears.

(Bull Run, Virginia – View of the battlefield)

Sullivan Ballou was killed a week later at the First Battle of Bull Run.

In this 150th anniversary of those horrible, bloody years of the American Civil War, please take a few minutes and listen to Sullivan Ballou’s heart-felt sentiments.

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[1] The music in the background is entitled Ashoken Farewell.

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