Peter

Some bacterial genomes are quite large. A few are larger than the smallest eukaryotic genomes.

Many species of cyanobacteria are complex, multicellular organisms [Multicellular Bacteria]. Those species tend to have large genomes.

Recently Degan et al. (2013) sequenced the genomes of six new cyanobacteria species and one of them turns out to have a large genome.¹ (see Contradictory Phylogenies for Cyanobacteria for more information on that paper.) The species is Scytonema hofmanni and its genome is 12,073,012 bp in size. It has 12,356 potential protein-coding genes. If all of them are correctly identified then the total, counting non-protein-coding genes, is likely to be 12,500 genes. That's a record for prokaryotes.

Half of these genes are only found in Scytonema and that's very strange.

There are bacteria with larger genomes, notably the soil bacterium Ktedonobacter racemifer with a genome size of 13,661,586 bp.

For comparison, the genome of the yeast, Saccharomyces cerevisiae, is 12,156,677 bp in size and it has 6,200 genes.

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Photo Credit: Scytonema hofmanni from cyanobacteria slides.

1. Some of you might be under the impression that I give a shit about Norm Pace and his attempt to banish the word "prokaryote" (Pace, 2009). Don't bother to try and convince me because it requires that I accept the false Three Domain Hypothesis and that ain't gonna happen.

Dagan, T., Roettger, M., Stucken, K., Landan, G., Koch, R., Major, P., Gould, S. B., Goremykin, V.V., Rippka, R., de Marsac, N.T., Gugger, M., Lockhart, P.J., Allen, J.F., Brune, I., Maus, I., Pühler, A. and Martin, W.A. (2013) Genomes of stigonematalean cyanobacteria (Subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids. Genome biology and evolution 5:31-44.
[doi: 10.1093/gbe/evs117]

Pace, N.R. (2009) Time for a change. Nature 441:289. [doi:10.1038/441289a]

The cyanobacteria are interesting for a number of reasons. They have a complex photosynthesis pathway with two separate phostosystems and an oxygen evolving complex. That means they can use water as an electron donor and NADP^⊕ as an electron acceptor.

Cyanobacteria probably played an important role in creating an atmosphere with significant levels of oxygen but, contrary to some speculation, they almost certainly arose fairly late in the history of life (i.e. after 500 million years). Cyanobacteria make up a significant proportion of life in the ocean. Primitive cyanobacteria gave rise to chloroplasts in modern plants and algae.

Read more »

Thanks to an alert reader, I was put on to this paper in PNAS. It's from a team at Washington U. in St. Louis, and my fellow Cardinals fans are definitely stirring things up in the debate over "junk DNA" function and the ENCODE results. (The most recent post here on the debate covered the "It's functional" point of view - for links to previous posts on some vigorous ENCODE-bashing publications, see here).

This new paper, blogged about here at Homologus and here by one of its authors, Mike White, is an attempt to run a null-hypothesis experiment on transcription factor function. There are a lot of transcription factor recognition sequences in the genome. They're short DNA sequences that serve as flags for the whole transcription machinery to land and start assembling at a particular spot. Transcription factors themselves are the proteins that do the primary recognition of these sequences, and that gives them plenty to do. With so many DNA motifs out there (and so many near-misses), some of their apparent targets are important and real and some of them may well be noise. TFs have their work cut out.

What this new paper did was look at a particular transcription factor, Crx. They took a set of 1,300 sequences that are (functionally) known to bind it - 865 of them with the canonical recognition motifs and 433 of them that are known to bind, but don't have the traditional motif. They compared that set to 3,000 control sequences, including 865 of them "specifically chosen to match the Crx motif content and chromosomal distribution" as compared to that first set. They also included a set of single-point mutations of the known binding sequences, along with sets of scrambled versions of both the known binding regions and the matched controls above, with dinucleotide ratios held constant - random but similar.

What they found, first, was that the known binding elements do indeed drive transcription, as advertised, while the controls don't. But the ENCODE camp has a broader definition of function than just this, and here's where the dinucleotides hit the fan. When they looked at gene repression activity, they found that the 865 binders and the 865 matched controls (with Crx recognition elements, but in unbound regions of the genome) both showed similar amounts of activity. As the paper says, "Overall, our results show that both bound and unbound Crx motifs, removed from their genomic context, can produce repression, whereas only bound regions can strongly activate".

So far, so good, and nothing that the ENCODE people might disagree with - I mean, there you are, unbound regions of the genome showing functional behavior and all. But the problem is, most of the 1,300 random sequences also showed regulatory effects:

Our results demonstrate the importance of comparing the activity of candidate CREs (cis-regulatory elements - DBL) against distributions of control sequences, as well as the value of using multiple approaches to assess the function of CREs. Although scrambled DNA elements are unlikely to drive very strong levels of activation or repression, such sequences can produce distinct levels of enhancer activity within an intermediate range that overlaps with the activity of many functional sequences. Thus, function cannot be assessed solely by applying a threshold level of activity; additional approaches to characterize function are necessary, such as mutagenesis of TF binding sites.

In other words, to put it more bluntly than the paper does, one could generate ENCODE-like levels of functionality with nothing but random DNA. These results will not calm anyone down, but it's not time to calm down just yet. There are some important issues to be decided here - from theoretical biology all the way down to how many drug targets we can expect to have. I look forward to the responses to this work. Responses will most definitely be forthcoming.

Back in February 2001, noted ornithischiphile Pete Buchholz accused ducks of being boring. How dare he. I could only respond… “Errm… the evolution of carpal spurs and knobs, extreme...

-- Read more on ScientificAmerican.com

Here’s the first in our series answering your questions about the project. We start with a question from Maggy Wassilieff, who wants to know about the tuatara population living on North Brother Island in the Cook Strait: Could you comment on the current understanding of the Brothers Is Tuatara? Is it a separate species? How [...]

[Click on the headline above for the full story]

In my column this week for the New York Times, I write about the discovery of record-breaking viruses called pandoraviruses. They’re 1000 times bigger than a flu virus and have almost 200 times as many genes–over 2500. That’s twice as many genes as the previous giant-virus record holder, which I blogged about in 2011.

These giant viruses are important to our understanding of what the difference is–if any–between viruses and the rest of life. But they’re also part of a bigger story, one that inspired the title of my recent book A Planet of Viruses. Viruses are the most common life form on Earth, they are by far the most genetically diverse, and we have barely started to explore the viral frontier.

That frontier includes giant viruses–and tiny ones, too. Just last week, for example, Jessica Labonte and Curtis Suttle of the University of British Columbia published a survey of another group of viruses called single-stranded DNA viruses. Their ranks include parvoviruses, which cause an infection sometimes known as the Fifth Disease. If you’ve gotten it, like I did a few years ago, you know that feeling it provides you that someone has been using your body as a punching bag for hours.

The ranks of single stranded DNA viruses include many other pathogens of plants and animals, plus others that infect bacteria. They are exquisitely small, with as few as three genes.

Labonte and Suttle searched through sequenced of DNA that have been trawled up from sea water at a few sites around the world. They found a lot of single-stranded DNA virus genes, which they compared to the seven known families of the viruses. They realized they have probably discovered 129 new families.

Just another week on the viral frontier…

The writer Megan McArdle asserts that Republicans have about a 75 percent chance of winning the White House in 2016, because "voters just get tired after eight years."

"What Happened to Blog Syn?"*

I get asked that question a few times every week. With questions about scientific (ir)reproducibility and data integrity popping up everywhere, it would seem apropos to resurrect the blog from its months-long slumber. So why aren't we posting?

Changing Circumstances: Five synthetic chemists ran most of the experiments for the first three posts.
Where are they now?

- One moved to another country, and hasn't started in his new lab
- One defended his Ph.D., and moved to another state
- One passed his qualifying exams, and wrote a bunch of papers for a new lab
- One faced a daunting funding situation at his small company, along with changes in work responsibilities
- (I don't know where the last person is...!)

So . . . life happened.

Time: The process of coordinating and writing a Blog Syn entry takes a while. Let's compare:

Just Like Cooking: Read interesting paper, dig up literature, make some graphics, edit, post.
Time: 20-60 minutes

Blog Syn: Read interesting paper, discuss with Twitter community and coworkers, read supporting literature and SI, coordinate across multiple time zones by email, order reagents, run experiments, purify, analyze, compare data, coordinate response by email / Skype / Twitter, construct post, peer edit, post.
Time: 2-4 weeks

Resources: We have no formal funding model. At present, our labs bear Blog Syn's costs, and that's OK for reagents you have just sitting around. It becomes dicey, though, to convince purchasing managers to order unusual reagents for your pet projects.

People: Despite multiple attempts to recruit chemists to the cause, we've not added anyone new to our roster. I've sent out at least three separate email blasts, had some nibbles, but no one has committed. I feel it would be disingenuous to run each experiment in triplicate myself, since that only proves that I could repeat all my own mistakes.

I think what's happening to Blog Syn is what happens to all volunteer organizations over time. Life happens. People move. Interests shift and change. Resources dwindle. The message and mission grow muddy.

*HELP WANTED: I'd really like to keep this going; I have preps picked out to try, folks to review and publicize posts, even some potential funding to fall back on. So, who's with me? Who wants to help revitalize Blog Syn?

If you've been dragging your heels and wish to get involved, don't hesitate to contact me!
Operators are standing by...

The year is half over, so let’s look at the current status of creationism. In one sense it can be said to be flourishing, because there are millions of wandering ignoramuses, but we’re not concerned with them — only with the major players, particularly the Discoveroids, described in the Cast of Characters section of our Intro page.

Our principal concern is with the Discoveroids because they’re the most politically active of all creationist groups, and their goal, never explicitly stated but inherent in their wedge strategy, is establishing a theocracy and suppressing all of science. We think of most other creationist outfits as relatively harmless peddlers of nonsense, like Answers in Genesis (AIG). Groups like that are discussed in our blog mainly for amusement.

Speaking of amusement, it’s quite amusing to note that AIG’s grandiose plans for building a super-duper replica of Noah’s Ark appear to be foundering in a flood of financial disappointments — see Ken Ham Keeps Getting Pounded.

Turning our attention to the Discoveroids, when the year began they were bursting with optimism — see Discovery Institute Sees a Big Year Ahead. Their brain-dead followers were filing “academic freedom” bills in several state legislatures and the future looked rosy — for those who yearn for a new era of Dark Ages ignorance.

Notwithstanding their expectations in the arena of legislation, the Discoveroids have had one defeat after another. Their “academic freedom” bills have failed to pass in Arizona, in Colorado, in Indiana, in Missouri (two bills), in Montana, in Oklahoma (two bills), and in Texas. No other Discoveroid bills are currently pending.

There’s still Stan Bingham’s North Carolina Bible Class Bill. It’s not a Discoveroid bill, so in the context of how they’re doing, it doesn’t count. It is, however, a bill to promote creationism, so we’re tracking it. Back in February it was referred to Committee on Rules and Operations of the state Senate. There have been no hearings or votes, and nothing’s scheduled. The legislative session was scheduled to adjourn in “early July,” but they’re still in session. Nevertheless, there seems little hope for Bingham’s bill — at least this year.

The only success the Discoveroids have enjoyed is in Louisiana, where the legislature once again refused to repeal the Louisiana Science Education Act — see Louisiana Victory for Creationism and Voodoo. Here we’re using the term “success” loosely, as they barely held on to an earlier legislative accomplishment — one of their few.

In the arena of courtroom litigation, the Discoveroids’ biggie was the David Coppedge case, and they lost that one — totally. See David Coppedge Trial: Final Order Issued, and then The David Coppedge Case: It’s Over. We’re not aware of any other court cases they were promoting this year.

The endless case of John Freshwater is about to be decided by the Ohio Supreme Court. It’s not a Discoveroid case, but it involves a creationist in a public school, so it’s been interesting to follow. Our last post on that was months ago — Freshwater Oral Arguments Today.

And then there’s a lingering litigation mystery. We’ve never been able to learn what happened with John Oller’s litigation against the University of Louisiana at Lafayette, where he is (or was when the suit was filed) a professor. See Louisiana Creationist Professor Sues University. That wasn’t a case the Discoveroids supported; Oller was too hard-core for them. But he had other supporters — see Ken Ham Supports John Oller’s Lawsuit. His case may have been settled by now, one way or another. If anyone knows anything about it, please let us know.

[Addendum: One of our clandestine operatives told us about this link to the docket of court pleadings in Oller v. Roussel et al. And here's an updated docket: Oller v. Roussel et al, indicating that a jury trial is scheduled to start on 21 Jan 2014. Most of the pleadings require a subscription, but you can see the answer. It's not terribly informative (the university denies all liability). Anyway, now we know that the case is still pending.]

Other than that, as we reflect on the first half of this year, there really hasn’t been any creationist success, and there’s been little serious activity worth noting. Oh, here and there we see an occasional school board make fools of themselves, but such comedies are mostly of local significance. So at this point we can report that 2013 has been a total disaster for what we might term “institutional creationism.” May it always be so.

Copyright © 2013. The Sensuous Curmudgeon. All rights reserved.

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Hey everyone! Twi big announcements today. First, we have just passed the halfway point in my Kickstarter campaign, and to commemorate this milestone, I have some amazing news: There is a new tier at the $175 level where you can get your hands on your very own handmade Pineapple Maki Plushie!

WHAAAAAAAT?! 

This limited edition, one-of-a-kind item (made by the amazing Tally Heilke) is marked with a special backer’s patch and comes with a signed certificate of authentication.

Supplies are limited, and they may not be available ever again, so go claim one now! Booyah!

 

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In science news: Remember the University of Queensland pitch drop experiment? It still hasn’t dropped yet. But what I never mentioned was that there was another pitch drop experiment running at Trinity College in Dublin. That’s right. It’s like in the film, Contact, when you find out there was another machine built in secret all along. Except it wasn’t a secret. I just never told you.

Similar to Queensland, the Trinity College drop had a camera trained on their experiment, and yesterday it all paid off. We have a pitch drop. According to RTE News/Ireland, the drop fell last Thursday in a moment celebrated by grass and wet paint watchers everywhere.

It’s pretty damn cool! What  surprised me was how fluid it still was at the moment of dropping. I had expected that the drop would just suddenly break at one point from a combination of its weight and thinness of the connection, but the video shows a fluid drop the whole way though.  Incredible stuff.

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July 18th, 2013: This Is How You Die is out now! It's an awesome book I helped edit! I keep saying how great this book is! I think you should buy it! THIS IS HOW YOU DIE make magic happen via capitalism In non that-book news, I am in San Diego today, tomorrow, and all weekend for the San Deigo Comics Convention! Here's where to find me! One year ago today: in which i present a sincere argument of how fanfiction will save the future – Ryan

TheologyGrams shared this gem:

I shared another Doctor Who-related diagram from that blog once before. There are several other wonderful items that have since appeared there, and so here are a couple more:

Apophatic Theology Explained:

How to work out where Mark’s Gospel ends:

I’m not even half-way into this program and there’s already talk of bringing me back next year as a TA. I suppose I should be flattered, but really, given the circumstances, I feel awkward more than anything else.

You see, the World’s Most British Person* and I were attending a cocktail party with one of the program-directors, who was aggressively trying to recruit both of us.

“What we need are TAs of great passion and intelligence, who put our institution’s best foot forward!” she enthused. “Like you,” she said, turning to the World’s Most British Person; “a student at one of the world’s top universities**.” And then she added: “Or someone who represents our commitment to diversity; like you Jaime.”

“Ah…thanks,” I replied, and sipped generously of my Alsatian wine.

Diversity. So this is what I have come to, is it? The moment that I have dreaded since I first came out: having all of my other accomplishments in life subordinated to the mere fact of my existence as what I am. The token tr*nny.

I must admit, the experience was almost surreal for me. All talk of “residual male privilege” aside, the fact of the matter is that I grew up appearing outwardly as a heterosexual, white, native-born, middle-class, man in a first-world country. And whatever other words get applied to people with such a background, I can guarantee you that “diverse” is not one of them.  Suddenly finding yourself (if only to some limited extent) on the outside looking in is disorienting to say the least.

Rationally though, I can’t quite figure out why this incident bothers me so much. I mean, it’s a bit condescending to be sure, but it’s not the first bit of favouritism I’ve ever been shown. To cite an obvious example, I managed to get all of the way through undergraduate university without paying tuition due exclusively to the fact that my father was a professor there. Then, as now (only moreso) I was being granted a selective advantage not because of my own accomplishments, but because of the immutable circumstances of my own existence. And that was a much bigger advantage than this one***.

And that, of course, is that elephant in the room whenever people discuss “affirmative action.” It’s not that “mainstream society” doesn’t benefit from it, it’s that nobody ever sees fit to point-it-out to them when they do. The only functional difference between my unearned advantages before transition and now is that now I have fewer of them and I feel guiltier about them.

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*He is tall, pale and possessed of a name which rivals “Benedict Cumberbatch” itself for Patrician flair.

**He is, of course, an Oxonian.

***And in my defense, I did feel pretty bad about this one too.

Steven Zimmer, a member of the board of the under-assault Los Angeles Unified School District, lays it on the line:  Class size is important, and legislative efforts to expand class size in public schools are intended to sabotage public schooling — and that action harms students.

Description of the video at YouTube from the OTL Campaign:

Small class size isn’t about protecting teachers’ jobs or making their work easier — it’s about providing every student with quality attention in the classroom. Steve Zimmer, Board Member of the Los Angeles Unified School District and a former teacher, asks why we tolerate or dismiss crowded public school classrooms when charters and private schools use small class sizes as a selling point?

More:

• Steve Zimmer on Why Class Size Matters (dianeravitch.net)
• Fresno Unified officials plan for extra $15 million (fresnobee.com)
• LAUSD Debating New School Funding Options (losangeles.cbslocal.com)
• Does class size affect the learning process? (voxxi.com)
• ARIZONA: Charter schools seeing growth across the state (charterpulse.com)
• Call Your Representative Today! And Tomorrow Too! (dianeravitch.net)
• Local districts shouldn’t bear burden of funding charter schools (bangordailynews.com)
• Charter schools offer scant edge over neighborhood schools: study (news.terra.com)
• Tend to Wake County schools (newsobserver.com)
• Learning Journal Week 2 (chiraphatch.wordpress.com)

 

Filed under: Classroom management, Classroom size, Education, Education Administration, Education reform, Teachers, Teaching Tagged: Class Size, Education, Education reform, Los Angeles Unified School District, school boards, Steven Zimmer, Teachers, Teaching

If you live in the Northern Hemisphere and go outside around midnight in the summer, you’ll see a big W made of five brightish stars in the northeast. That’s Cassiopeia, the constellation of the queen. Due to geometric circumstance, we are looking into the plane of our galaxy when we peer in that direction. That means we’re looking into a region of space that has more stars, more gas, and more dust than average.

Which means it’s a good place to look for interesting objects. And in fact it’s where you will find the gorgeous nebula Sharpless 2-188, the gas cast off by a dying star:

This image was taken by my friend Travis Rector (and Heidi Schweiker) using the Kitt Peak 4-meter telescope. They used two filters; one shows hydrogen gas (orange) and the other oxygen (cyan). I highly suggest you grab the 4,900-by-3,800 pixel version, or at least the 1,200-by-940 pixel image, because wow.

Sh2-188 is what we call a planetary nebula, a bit of a misnomer since the first that were discovered looked small, disk-shaped, and slightly greenish through a telescope. Now we know they’re formed by the winds from dying stars, vast gales of gas expelled as the star sheds its outer layers and exposes its small, hot core. The leftover star, called a white dwarf, is so hot it blasts out ultraviolet light, enough to cause the gas to glow.

Planetaries come in fantastic shapes, mostly due to the way the wind from the star changes over time and interacts with previously blown-out material. But Sh2-188 is different, even by the standards of the planetary nebula menagerie. It’s highly asymmetric. Even though you can see it makes a complete circle (well, oval), one side is far brighter and more interesting-looking than the other.

This is almost certainly due to the culprit star itself, screaming through space at high speed. It’s not 100 percent clear which star is at the heart of this nebula, mostly because there are so many to choose from! But there is a faint star down to the lower left of the inside of the cloud, faint and not at all distinguishable by eye from any of the others, that is most likely the actual “central” star. It’s blue—expected for the hot, dense, cinder needed to light up this gas—and about the right brightness.

Also as expected, measurements over time indicate the star is moving through space toward the lower left, probably at well over 100 kilometers (60 miles) per second. That would explain much of why this nebula is so asymmetric; as the star (and its wind) rams through the gas in space, the stuff in the direction of travel piles up, just like a snowplow pushing through snow. It’s also possible that there’s just more stuff in between the stars in that direction, so there is more material to pile up. But either way, the speed of the star is the major reason this planetary is so unusual.

I found this picture browsing through Travis’ gallery, and even before I read his description I thought to myself, “Huh. That looks familiar!” and sure enough, Travis had the same thought and mentioned it in the caption.

Does it look like the logo for any browser you might be using?

Once you see it, the resemblance is pretty good. I can see ears, a nose, the tail, even the foreleg! And while it may not actually be on fire, the surface temperature of the stars is far hotter than the Sun. Of course, it’s in the constellation of Cassiopeia, the queen, not Vulpecula, the fox, but still. At 60 trillion kilometers in diameter, it makes a heckuva logo.

Mozilla, you may have a new direction for your branding …

Related Posts:

The Flaming Skull Nebula. Seriously.
A Dying Star With the Wind in Its Hair
A Glowing, Bubbly Bauble in Space
A Star on the Edge of a Weird, Lovely Death
The Green Ghost of a Distant Dead Star

Way back in the old days, I was a frequent participant in the forums at the Christian Apologetics and Research Ministries. Matt Slick, who owns the site, even asked me to be co-moderator of the evolution/creationism forum along with creationist Penny Fryman. So I read with particular interest this essay at Hemant’s blog by Rachael Slick, Matt’s daughter who is now an atheist. Some of it is pretty heartbreaking, including this excerpt from her journal that was written when she was 9:

I’m hopeless.

Oh boy. I’ve got a lot to work on. I try to be obedient but it’s so hard! The more I read, the more I realize how bad I am! My problem is that when things don’t make sense to me, I don’t like them. When Dad gets mad at me for something, everything makes perfect sense to me in my mind, so I tend to resent my parents’ correction.

I have just realized that I yearn to please the lord, but why can’t I? I just can’t be good! It seems impossible. Why can’t I be perfect?

And this:



As my knowledge of Christianity grew, so did my questions — many of them the “classic” kind. If God was all-powerful and all-knowing, why did He create a race He knew was destined for Hell? How did evil exist if all of Creation was sustained by the mind of God? Why didn’t I feel His presence when I prayed? 


Having a dad highly schooled in Christian apologetics meant that every question I brought up was explained away confidently and thoroughly. Many times, after our nightly Bible study, we would sit at the table after my Mom and sisters had left and debate, discuss, and dissect the theological questions I had. No stone was left unturned, and all my uncertainty was neatly packaged away.



Atheists frequently wonder how an otherwise rational Christian can live and die without seeing the light of science, and I believe the answer to this is usually environment. If every friend, authority figure, and informational source in your life constantly repeat the same ideas, it is difficult not to believe they’re onto something. My world was built of “reasonable” Christians — the ones who thought, who questioned, who knew that what they believed was true. In the face of this strength, my own doubts seemed petty. 


But all is well that ends well:

Someone once asked me if I would trade in my childhood for another, if I had the chance, and my answer was no, not for anything.
 My reason is that, without that childhood, I wouldn’t understand what freedom truly is — freedom from a life centered around obedience and submission, freedom to think anything, freedom from guilt and shame, freedom from the perpetual heavy obligation to keep every thought pure. Nothing I’ve ever encountered in my life has been so breathtakingly beautiful. 



Freedom is my God now, and I love this one a thousand times more than I ever loved the last one.

That passage is hauntingly beautiful and eloquent. Please read the whole thing. It’s very powerful and moving.

I rode on a roller-coaster for the first time last weekend. It may come as a surprise to some of you that I’ve never done this before; surely any child to grow up in North America within the last fifty years must have been on at least one roller-coaster prior to the age of ten! But it was never an ambition of mine as a child, for the very simple reason that I was (and am) a coward*. This time was different though; this time, I figured that, being as I am in Europe, I’m already about eight thousand kilometres east of my comfort zone anyways, so I may as well take advantage of the opportunity to expand my horizons.

Thus it was that I accepted immediately when a group of us were offered a chance to visit Europa Park, the largest amusement park in Germany. And no sooner had I gotten there and witnessed the swirling array of its rides and attractions, then I began to wonder what the hell had possessed me to agree to all this.

Now, don’t get me wrong here; I believe in Newtonian physics, and I trust engineers, safety inspectors and insurance companies to do their jobs. Intellectually, I realize that I am far more likely to perish while riding my bicycle to work than I am to die on a roller-coaster.

And yet…

And yet, as I made that first, screaming, 4g descent down the Silver Star, I can guarantee that I was not thinking about physics or actuarial mathematics. Rather, the only thought going through my head at that moment was: “So this is how I’m going to die: a bloody pancake crushed beneath a heap of twisted metal.”   And I wish I could tell you that that feeling abated with subsequent rides, but no; it really, really didn’t.

The point that I’m trying to make, in a round-about sort of way, is this: there is a persistent belief out there which holds that somehow, rational understanding and emotional resonance are mutually contradictory, and that, knowledge can conquer fear.  I now know this, based on personal experience, to be false.

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*Indeed, I consider the fact that any child I am ever likely to have will probably one day want me to escort them onto a roller-coaster to be a relatively strong argument against having kids.

We recently wrote What Are We Learning from SETI?, in which we reported about a new project in the UK relating to the Search for Extra-Terrestrial Intelligence (SETI). Even with our Curmudgeon senses, it never occurred to us that the Discoveroids — described in the Cast of Characters section of our Intro page — could do anything with it.

But we should have known better. Back in November of last year we posted Klinghoffer Opines on SETI, when Klinghoffer informed us:

Guillermo Gonzalez notes that “While these exoplanets are being discovered, astronomers are discovering additional constraints on the habitability of planetary systems.”

Yes, that Guillermo Gonzalez. If the name doesn’t ring a bell, see Ball State University Hires Guillermo Gonzalez. He’s a co-author of the classic creationist book, The Privileged Planet, a “fine tuning” argument applied to Earth. The claim is that we’re alone in the universe, because that’s how the designer — blessed be he! — wanted it to be.

Klinghoffer also said this about SETI:

In the total absence of evidence for actual life out there, the more common those conditions are, the more special — i.e., not readily evolved by natural means alone — life must be.

Okay, remembering that the Discoveroids think SETI is a waste of time, we turn to their blog and find this: Royal Support for ID: UK Funds SETI Project. They say, with bold font added by us:

The Search for Extra-Terrestrial Intelligence (SETI) is predicated on a notion familiar to theorists of intelligent design: that it is possible to distinguish intelligent causes from natural causes.

[...]

Ironically, though, most SETI supporters are ardent Darwinians. They just don’t get it. They call ID religion, but find its principles very useful for detecting intentional design from the intelligence of aliens.

The very real differences between SETI and the Discoveroids’ “theory” are explained here by Seth Shostak of the SETI Institute: SETI and Intelligent Design. He says:

In short, the champions of Intelligent Design make two mistakes when they claim that the SETI enterprise is logically similar to their own: First, they assume that we are looking for messages, and judging our discovery on the basis of message content, whether understood or not. In fact, we’re on the lookout for very simple signals. That’s mostly a technical misunderstanding. But their second assumption, derived from the first, that complexity would imply intelligence, is also wrong. We seek artificiality, which is an organized and optimized signal coming from an astronomical environment from which neither it nor anything like it is either expected or observed: Very modest complexity, found out of context. This is clearly nothing like looking at DNA’s chemical makeup and deducing the work of a supernatural biochemist.

Let’s get back to the Discoveroids’ article. It’s all balderdash, so we’ll jump right to their final paragraph:

Any alien detecting the effects of our civilization — say the Voyager spacecraft, now approaching interstellar space — would be justified in concluding it to be a product of intelligence. If it would be absurd for aliens to dream up a theory that the spacecraft “evolved” out of interplanetary dust, it would surely be just as absurd were SETI researchers to find an alien civilization and attribute it to natural causes. SETI researchers are ID advocates in spite of themselves.

So there you are. The Discoveroids claim that their nonsensical theory of intelligent design is great science because it’s endorsed by SETI researchers. Yes, and crop circle researchers can similarly claim that their bizarre beliefs are validated by geometry, just as ancient astronaut “theorists” are validated by archeology, and moon-landing denialists are validated by … whatever.

Copyright © 2013. The Sensuous Curmudgeon. All rights reserved.

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Yesterday I wrote about why negative controls are important in a genome-scale search for functional DNA. Today, I’ll discuss the main focus of our recent work: understanding what makes a piece of DNA functional.

The particular DNA I’m interested in is known by not very functional term ‘cis-regulatory’ DNA – a term that requires six syllables, an italicized Latin prefix, and a hyphen. This is DNA that is crucial in gene decisions: cis-regulatory DNA helps to control when, where, and how much genes are expressed. This happens because cis-regulatory DNA serves as a landing pad for ‘transcription factors’, proteins that land on cis-regulatory DNA and control the expression of nearby (or sometimes not so nearby) genes.

The question that haunts me is this: why don’t transcription factors get lost? My worry follows from these three observations:

1. Transcription factors recognize very short segments of DNA. To give you an example, the transcription factor I study, the eye development factor Cone-rod homeobox (Crx), recognizes slight variations of the 8-base sequence CTAATCCC.

2. Large eukaryotic genomes are packed with millions of copies of these short sequences. The 8-base Crx recognition site occurs more than 6.6 million times in the mouse genome.

3. Only a small fraction of all potential transcription factor recognition sequences are actually bound by transcription factors. In the case of Crx, only about 14,000 of 6.6 million 8-base recognition sequences are bound by Crx in the genome.

I’ve illustrated the problem below. On the left is an image of the transit of Venus across the Sun. On the right, the blue circle shows the small fraction of Crx recognition sites that are bound.

So yes, I’m serious – why don’t transcription factors get lost in giant genomes?

There are two primary answers (not mutually exclusive) that people typically turn to:

Hypothesis A: Chromatin context is everything. In any given cell, most of the genome is inaccessible, wrapped up into large, compact regions of dense chromatin. This reduces the transcription factors’ search space, so they don’t get lost.

But if context is the answer, how do the right parts of the genome get left exposed?

Hypothesis B: DNA grammar provides specificity. Short 8-base pair recognition sequences are not enough; true functional sites consist of rare, highly specific combinations of short recognition sites. The millions of spurious sites in the genome do not have the right DNA grammar, and they are not bound.

But if grammar is the answer, why do transcription factors seem to non-specifically bind all over the place?

We set out to resolve this dilemma by testing the cis-regulatory function of two types of genomic DNA:

Bound DNA: DNA segments with Crx recognition sites that are bound by Crx in the genome (i.e., ChIP-seq peaks).

Unbound DNA: DNA segments with equal numbers of good Crx recognition sites, but which are not bound by Crx in the genome.

Importantly, we tested these DNA pieces outside of their native genomic context, in the very permissive context of plasmids.

So, under Hypothesis A, both bound DNA and unbound DNA should be functional, because they have both been removed from any genomic context and placed on plasmids. The context is now the same for both classes of DNA.

Under Hypothesis B, bound DNA should be more functional than unbound DNA, regardless of context.

We tested large numbers of bound and unbound DNAs in our massively parallel¹ functional (i.e., reporter gene) assay. (We did this in the dissected whole retinas of baby mice.) The result came as a surprise to me, because I was betting on Hypothesis A. But it turns out that bound DNA differed from our random DNA distribution (showing function), while the unbound DNA largely resembled the random DNA distribution (showing non-function).

You can see this in these histograms from Fig. 1 of our paper. In the first panel, bound DNA distribution is in blue, the random DNA distribution is in green, and the level of gene expression is shown on the x-axis:

In the next panel, unbound DNA is in blue, and random DNA is in green – notice that these two largely overlap (except in the left tail):

What this means is that the distinction between functional (bound) and non-functional (unbound) DNA is independent of context, at least to a large degree. The information that distinguishes function from non-function is therefore locally encoded in the short DNA regions (84 bases) that we tested.

So the answer must be hypothesis B, DNA grammar, right? Well, maybe, but so far we have been unable to find any obvious grammar. We’re now looking at more subtle structural DNA features that could account for the difference between function and non-function.

One final point – without our random DNA negative controls, our empirical null distribution, we would have drawn a very different conclusion. Unbound DNA would have looked very functional, just not quite as functional as bound DNA. But in fact the unbound DNA, which has lots of Crx recognition motifs, behaves much like our random DNA, which has very few Crx recognition motifs, and that means that most of what the unbound DNA is doing is non-specific, the result perhaps of biological noise.

Our paper: “Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks”, PNAS July 16, 2013 vol. 110 no. 29 11952-11957.

1. Yes, ‘massively parallel’ is a technical term, one that has a different meaning from ‘high thoughput’.

• Title: Global collapse of molecular clouds as a formation mechanism for the most massive stars
• Authors: N. Peretto, G.A. Fuller, A. Duarte-Cabral, A. Avison, P. Hennebelle, J.E. Pineda, Ph. Andre, S. Bontemps, F. Motte, N. Schneider, S. Molinari
• First Author’s Institution: Laboratoire AIM, CEA/DSM-CNRS-Universite Paris Diderot, IRFU/Service d’Astrophysique, C.E. Saclay, France

The formation of massive stars is still an intense topic of debate. Two theories currently stand.  The first theory predicts that molecular clouds undergo fragmentation, forming compact cores, which subsequently accumulate in mass. The second theory predicts that molecular clouds undergo global collapse, gathering matter from large scales much more rapidly. The first theory takes place slowly over time, whereas the second theory takes place ‘instantaneously.’

Observations are difficult because massive star forming regions are heavily obscured by dust – invisible in the optical and near infrared. The trick is to look at much longer wavelengths.  Today’s paper does just that, using the Atacama Large Millimeter Array (ALMA) in Chile to observe the birth of a massive star in submillimeter wavelengths. At 500 times the mass of the Sun and 1 million times brighter, it is the largest forming protostar ever seen in our galaxy.

The star-forming core in question lies at the center of the infrared dark cloud SDC335.579-0.292. Oh astronomers and their naming schemes! Such clouds appear dark in comparison to the bright (infrared bright, that is) galactic plane.  At 3.25 kpc from the Sun, little gas has been ionized in this star-forming core. Since massive O stars reach temperatures so hot they ionize their outer atmospheres, this ensures that the cloud is relatively young, with no massive stars yet formed.

Peretto et al. used publicly available data from the Spitzer Space Telescope, as well as the Herschel Space Observatory. They then observed the infrared dark cloud with ALMA in Chile – the most powerful radio telescope in the world.

Observations revealed a network of six filaments leading to much brighter sources in the center of the cloud – central star forming cores. Along these filaments, matter is being pulled into the central core. We are seeing massive stars at the beginning of their formation!

Both cores, so-called MM1 and MM2, are 0.054 pc and 0.057 pc in diameter, respectively. Their inferred core masses are 545 and 65 solar masses, respectively. MM1 is the most massive, compact protostellar core ever observed in the Galaxy. It is likely to be an O-type star progenitor. In addition to both cores, a 1000 solar mass cluster should emerge with approximately 320 total stars. Thus, an OB cluster similar to the Trapezium cluster in Orion is likely to be in the early stages of formation.

The team determined two scenarios in which MM1 is likely to have formed. 1.) the material was initially part of a much larger volume that then collapsed to form the volume we observe today.  2.) the material currently lying in MM1 initially had the same diameter as observed today.  It then accreted mass from its surroundings over time.

Both of these scenarios require large-scale – as opposed to local – collapse to form MM1. The cloud core begins to collapse inwards, forming the massive protostar, while at the same time the surrounding gas cloud collapses on a larger scale with the inflowing gas rushing inward (at a rate of 0.4 km/s) along the filaments.

“It is always adventurous to draw general conclusions based on a single example,” explains Peretto in the paper. While this is the most massive star we have yet to see form, there are several other sources that hint at massive star formation.  All of which suggest that large-scale infall plays a major role in building massive stars.

 

I have many pet peeves. One of them concerns the people who build paths and walkways. If you're going to spend a lot of money constructing fancy walkways, then it makes sense to put a little thought into where you're going to put them. As a general rule, you should put the walkway where people are going to walk.

A few years ago (2008), the University of Toronto spent a million dollars on constructing new pathways throughout the downtown campus. The new paths mostly followed the old paths but there were places where that didn't make sense. As I reported back then [If you build it, will they follow?], the old path didn't line up with the new ramp to my building (see photo below). The guys building the path agreed with me that the placement of the walkway made no sense but they were overruled by their supervisor who insisted that the alignment wasn't a problem. People would stay on the new walkway and they would be encouraged to do so by strategic placement of a big rock.



Can you guess what happened? That ramp is now the main entrance to my building for people coming up from the subway exit. Will they follow the path, taking a sharp right turn then a sharp left turn or will they cut straight across the grass making as much of a mess as before the new walkway was constructed?

Here's the result ...


Isn't that ridiculous? Just as predicted, people take the shortest distance between two points and if that means walking over the grass and making an ugly mess, then so be it. What's the point of spending a ton of money to make the campus look nice if this is the result?

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Here, I continue my look at The Rocks Don’t Lie by David Montgomery. I have not finished the book, but am rather writing these reviews as I read the chapters, so each one is fresh. Check out the end of the post for links to the other chapters as well as other related posts.

Chapter 2: A Grand Canyon

Those who are familiar with Young Earth Creationism know that a major contention is that the Grand Canyon can serve as evidence for a global flood.  For example, both Answers in Genesis and the Institute for Creation Research have several articles dedicated to the topic. (Just do a search on the sites–I have linked two examples. In the latter, the ICR author notes that the Grand Canyon is “Exhibit A for the flood model of geology.”)

Outline

David Montgomery notes this interest from young earth groups and so he dedicates a chapter to the topic. He uses his own exploration of the Canyon to lead into a discussion of the geological evidence. Some of the rock formations found there “require[d] both extreme heat and high pressure” to form (17). He turns to a brief explanation of radiometric dating: “…the age of a rock can be read like a geologic clock because radioactive isotopes decay at a fixed rate… If you know the half-life of an isotope–how long it takes for the remaining amount to decay–then the ratio of the parent-to-daughter isotope now in a rock tells you how long ago the rock crystallized” (17-18).

Next, Montgomery gives a fairly basic introduction to geology. He provides a brief overview of how one can note unconformities in the rock and how different formations cut across each other. These evidences, found in the Grand Canyon, show that it was formed by a series of events rather than one single event (20ff). Moreover, physical evidence of fossilized burrows from “wormlike animals” in the sandstone provides evidence against flood geology. “How could fragile worms have been crawling around on and burrowing into the seafloor during a flood powerful enough to remodel the planet? The biblical flood would have had to have dumped more than ten feet of sediment every day for a whole year in order to have deposited the thousands of feet of sediment exposed in the canyon walls” (22).

More evidence against flood geology is found in the way the sediments themselves were formed. First, the differing mass of types of silt, clay, sand etc. make it difficult to believe that they could have been mixed together in a flood and then been deposited with uniformity of layers. Second, layers like that of white sandstone are composed of “fine-scale features” which “would have been obliterated if they had formed underwater… These dunes were made by wind” (25).

Finally, the fossils found within the Canyon present another difficulty. “If all the creatures buried… had been put there by the biblical flood, then why aren’t modern animals entombed among them? That the vast majority of fossils are extinct species presents a fundamental problem for anyone trying to argue that fossils were deposited by a flood from which Noah saved [at least] a pair of every living thing” (27).

Analysis

Montgomery has presented a number of extremely difficult problems for young earth interpretations of the Grand Canyon. In particular, the difficulty with the species of animals found buried seems intractable. My reason for noting this in particular is because flood geologists must assert that all the animal life is either descended from or prior to the animals in existence at the flood. Of course, if the Grand Canyon was formed by the flood, we should observe some of these extinct animals now–or at least recently. Yet for many, we do not. Why is that? A young earth perspective cannot simply assert that they died in the flood, for these would have been preserved in the flood.

The other problems Montgomery noted may sometimes be dismissed by advocates of young earth theories. In particular, Montgomery does little to defend radiometric dating, which is itself a major target of young earth views. For those interested, Davis Young’s The Bible, Rocks and Time gives an extended defense of radiometric dating, and Young writes from a Christian perspective on this topic. Overall, this chapter presents a number of problems young earth advocates must deal with.

Chapter 3: Bones in the Mountains 

Montgomery surveys briefly and selectively a history of Christian interpretation of the Genesis account and argues that some found room for less literal interpretations. Moreover, he points out that those who insist upon a literal reading of the text for Genesis must present reasons for not taking other references to the sky as a dome, etc. as non-literal (44-46, 50). Yet he also notes that the perspective from which the Bible is written (on earth) alleviates these difficulties–but these difficulties can only be alleviated by “allowing for figurative or allegorical interpretations” in which we “acknowledge… the fact that we live on a planet” (50).

Another difficulty with young earth views is presented, because the discovery of the New World revealed a massive amount of new species which the Ark would have had to carry. How does one fit all of these species onto the Ark? More importantly, how did these species get to the Ark and back to their homes in North America without leaving their ancestors’ bones behind in places other than their native lands? (42-43)

I have to say this chapter really surprised me, because Montgomery showed an appreciation for and interaction with Christian theology that I was not expecting. For just one example, he refused to set up the oft-rehearsed science-vs-religion rants that often accompanied discussions of Galileo. Instead, he explored the historical context, and noted that the ideas the church held were not necessitated by the text but were rather incorporated from Ptolemic ideas (49).

Conclusion

The Rocks Don’t Lie continues to impress me. Montgomery is careful to avoid overstating his case. More importantly, he seems to genuinely respect the beliefs of those whose writings he surveys and he shows a true concern for accuracy regarding some of the controversies. Thus far, he has presented a number of significant scientific challenges to a young earth paradigm, as well as noting the change and variety of perspectives within theology. Be sure to follow the blog for the next chapter(s)!

Links

Like this page on Facebook: J.W. Wartick – “Always Have a Reason”

Check out my review of a similar work by a Christian: The Biblical Flood. I think this book is vastly important and should be in every Christian’s library.

Be sure to browse my extensive writings on the “Origins Debate” over creationism, theistic evolutionism, and intelligent design (among other views) in Christianity.

Source: David Montgomery, The Rocks Don’t Lie (New York: W.W. Norton & Company, 2012).

SDG.

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Like lots of magicians and illusionists, I have always loved the idea of secret doors and hidden rooms.

The other day I found Secret Door Designs on the web. They send you all the stuff you need to make any door look like a bookcase. I measured up the door to my office, sent them the dimensions, and a few days later I received a mysterious package of fake books! A handyman and I put it all together (actually, to be honest, he did most of the work), and when it’s closed it looks like this….

 

And when it swings open, it looks like this…..

It was very easy to build (especially if you have someone else do it), and here it is being constructed…

Plus you can customise some of the books, thus allowing for a gag or two….

Anyway, I am not on commission or anything like that, I just thought that I would mention it because it seems like a rather lovely idea. Hope that you like it!

UPDATE: A few people have asked about handles and latches.  One of the shelves has a groove cut into it that acts as a handle, and the kit comes with a ball catch.

The blogosphere went wild last Friday when it was discovered that Texas Department of Public Safety troopers were confiscating tampons from women trying to watch the final Senate debate on extreme anti-abortion legislation at the Capitol in Austin. Then DPS officials said they had also stopped citizens from bringing more than a dozen containers with “suspected” feces and urine inside the Capitol. Religious-right groups and politicians latched on to that claim in their efforts to attack pro-choice activists. “My constituents don’t bring feces, urine, used tampons and bricks to throw at DPS,” state Rep. Steve Toth, R-The Woodlands, said in one sneering tweet.

But did pro-choice activists really try to bring containers of feces and urine into the Capitol to throw at DPS troopers (or anybody else)?

Today state Rep. Donna Howard, D-Austin, posted on Facebook her concerns about the claim:

Interesting. I sent a letter to DPS on July 15 in an effort to get more information regarding the report of suspected urine/feces being brought to the capitol during the hearing on HB2. Though KVUE reports that they received DPS’ response to my letter yesterday, I have yet to receive the response myself. This is the closing statement in my letter: “I am troubled that inaccurately distributed information may unfairly and unfavorably portray the thousands of citizens who legitimately and lawfully exercised their right of democratic participation–particularly since no evidence has been shown to substantiate the allegations related to these ‘suspicious jars.’”

The Texas Tribune has more about the DPS response to Rep. Howard’s letter:

In a letter to state Rep. Donna Howard, D-Austin, Texas Department of Public Safety Director Steven McCraw said that some visitors to the Senate gallery did attempt to bring jars of feces and urine inside during Friday’s debate on an omnibus abortion bill.

McCraw’s letter is a response to one that Howard sent Monday, in which she asked, among other things, for documentation of the actions. In response to that specific query, McCraw says that suspicious items were not confiscated and that people could store them outside the gallery or throw them in trash bags.

DPS did not take the names of anyone caught trying to bring feces, urine or other forbidden items inside the gallery, the letter reads, because “no crime had been committed, and it would be unreasonable to document names of visitors based on what they might or might not do.”

DPS officers interviewed by The Texas Tribune on Friday said they had not seen any feces or urine themselves, with several saying the interview was the first time they had heard of people trying to bring either item inside the gallery.

So let’s see if we’ve got this right. DPS troopers suspected that numerous people were trying to sneak bodily wastes into the Capitol to protest legislation, but they arrested no one and kept no evidence? Really? (And we’ve seen no evidence that backs up Rep. Toth’s claim that protesters brought those and other things into the Capitol to throw at DPS troopers.)

DPS troopers have been praised for their efforts to maintain order and protect visitors and lawmakers during last week’s emotion-filled protests and debate. We join others in applauding them. Our experience was that troopers largely acted professionally in a tense environment. If some individuals did plan to attack DPS troopers (or anyone else) with bodily wastes, bricks or whatever, that would be deplorable.

But like Rep. Howard, we’re troubled by the lack of evidence behind these charges. If there’s evidence to back up these claims, we will join others in condemning those who are guilty. But some on the right are using these unsubstantiated claims to discredit and defame the many citizens who were lawfully speaking out against government restrictions on the ability of women to decide whether and when to have children. That’s also deplorable.

I’ve often said my problem with organizations like Answers in Genesis is how liberal they are with the texts of the Bible.  I mean that sincerely.  They rightfully excoriate Old Earthers and evolutionists for attempting to bend scripture to their scientific penchants then they turn around and wildly abuse scripture to their own scientific preconceptions.  It says a lot about the evangelical mindset.  And so, we have this article published in Creation magazine by AinG.

Neil’s take-over of the New Zealand media scene continues apace. This weekend Neil and Graeme Hill from Radio Live had a chat about the project , Allan Wilson’s impact on evolutionary biology and where the tuatara fits into the New Zealand fauna.

[Click on the headline above for the full story]

Nour The Intern was assigned the task of monitoring Egypt’s rambunctious talk shows for an evening. This is her report.

After watching four consecutive hours of TV talk shows, followed by six hours online watching the talk shows I missed while watching TV – all telling me exactly how much I love and trust the army (a.k.a. The People's Army, The Patriotic Army and The Great Egyptian Army) whose generals and their predecessors and ancestors I ought to be writing a thank-you letter for – I was basking in the knowledge that helped my people save Egypt from terrorism and I wanted to buy a villa in Mountain View so I, too, could finally enjoy a quiet picnic with my wife.

What’s more baffling than my forgetting my financial status and my sexual orientation is the continuation of debate about whether or not there was such a thing as secular media bias, as if the tears of joy, the singing, the woo-hoos and the flag-waving that took place on-air moments after Morsi’s removal didn’t give anything away. 

Nowadays when talk show hosts are not repeating the same anti-MB rhetoric they used the night before - which at this point should be replaced with Taylor Swift’s We Are Never Ever Ever Getting Back Together to cut back on production costs - or finishing the sentences of their diverse guests, they are usually praising their viewers for their “sixth sense” that is their ability to detect the truth and corruption, their regime-toppling skills, their love for the military, and their donations to or investments in Egypt. They are not always nice, sometimes they are openly reproaching the viewers.

“The MB’s International Organization is having a meeting in Turkey, and you’re having iftar at home!” said an incredulous and disappointed Mohamed Sherdy, on AlQahera AlYoum, to his viewers. “All of this, and you are home eating iftar, thinking it’s all done,” he continued to scold them, begging the question: Why and how are Egyptians supposed to stop the MB from pondering recent political developments in Istanbul? And where would it be appropriate for them to break their fast for the meantime? 

“Well, I am not going to comment on this... since I’m the lame host, who is so ofar! (slang for over-the-top)” said Youssef el-Husseiny, mimicking his critics in a child’s voice, to his guest. “No, you’re loved a man,” his guest replied, in a conciliatory tone. El-Husseiny, whose face seems stuck in a perpetual smirk at his critics and the MB, had just finished off a long monologue recycling a conspiracy theory that says that the MB has infiltrated the Obama administration with Muslim aides and had anticipated some skepticism from his viewers, which is why he named the suspects on-air for the insultingly doubtful viewers to google them and see the undeniable evidence that is an unsourced 7-month-old Rose El-Youssef article for themselves. 

“I am not telling you Obama is MB, I would be a stupid man if I did,” he said. “This is not a joke... what is proven is that Obama sought help from the MB.”  

El-Husseiny went on with his monologue, which is just like Ibrahim Eissa’s minus the suspenders and Amr Adeeb’s minus the shouting, about how the MB are hated by just about everyone. Even more than half of the two million Gazans - whom it is believed that the MB planned to give Sinai to as a new homeland - have celebrated Fatah in Jan 2013, which means that they, too, loathe Hamas, i.e. the MB, he concluded happily, conveniently forgetting the fact that that celebration had followed a celebration of Hamas in the West Bank a month earlier and that the rallies were an attempt to ease the tensions between the two, and not public opinion polls.

Meanwhile on a different channel, Hala Sarhan was complaining to Tahani el-Gebali, who later rebuked her, and her colleagues, for not referring to the MB as the banned group that they are now “by popular decree,” about how some people didn’t like her map of the new, divided, Middle East, which she pronounced as the goal of the actually “US’s Dismantlement (of the Middle East) Plan” that is disguised as the MB’s agenda. 

Out of dreaded necessity, Sarhan then began to mumble, rather than read, the statements of the MB. “Ahmed Arif, the MB’s spokesman, said the era of the military imposing (its) opinion has ended...in the 60s” she read with a look of disdain. “You weren’t even born at the time,” she added, triumphantly, knowing that that’s an insult he couldn’t return. 

Lately, the most repeated media message regarding “the Brothers who call themselves “Muslims”,” whom the media ironically accuses of being takfiri (albeit rightly so), has been stressing the fact that the MB is part of an International Organization, a fact they appear to have suddenly rediscovered and are terrified of for largely unarticulated reasons. 

This international organization, according to them, is hell-bent on seizing power across the region, but doesn’t mind destroying the said piece of land on behalf of the Americans and the Zionists, in exchange for assistance and support to rule whatever is left. The main “proof” of that theory is that there used to be three strong armies in the region: The Egyptian army, the seventh/tenth/(insert favorite number) strongest army in the world, the Iraqi army, and the Syrian army. Where are the last two now? Finito. 

This makes the great Egyptian army the last piece in the puzzle and it’s stuck in their throat. Hence, your duty to love it. Admittedly, this would all sound a lot better coming from a bearded man, which is why there seems to be always a sheikh or a salafi, or a video of one, on demand to repeat whatever critical points a show host makes for reassurance. Some might argue that that’s using religion too, but that some should die. Since neutrality is a cowardly crime in all clear good vs. evil scenarios, which this is, according to popular belief.  

Then there is Raba’a. Although most people seem to be actively ignoring the sit-in, with a mixture of cold indifference towards the protesters and bored sympathy for the residents, some talk shows have taken it upon themselves to talk the islamists out of Raba’a or the army (and the people) into it.

Here’s a video of a talk show where a woman calls in to beg the military to forcibly break up the Raba’a sit-in because the disgusting, surely-not-Egyptian, protesters smell bad. The host nods his head in agreement, explains how unclean he too thought the sit-in is and then gives the government a 24-hour ultimatum: they either do/say something about it, or he will err- “confront them” about it every hour.

“(The Raba’a protesters) are our cousins, they will leave...they must leave...so  we can wreak vengeance on the MB leaders who are hiding behind them...(the Egyptian people) must come out in millions and take (the Raba’a protesters) in their arms,” an emotional Mostafa el-Gendy pleaded with the public via ONTV. He went on to beg the Salafis, “who used to sit with (him) and tell (him) that the Brothers were hypocrites,” to join him as well to avenge the martyrs.

Many like Ibrahim Eissa and Amr Adeeb prefered to address the Raba’a protesters gently, saying things of the following nature: You know, your leaders are pretty well-off. But what about you, my fellow citizen, sitting there under the scorching sun while fasting? Where was Safwat Hegazi when you were getting shot at, huh? Who dies at the end of the day? It’s always the little guy.

Others like Diaa Rashwan adopted the following religious approach: Give me one reason why Morsi is considered ‘Islamist’? You know he only said the word Israel twice in 59 speeches, and they weren’t even in a negative context. 

The most telling approach by far is Ahmed El Esseily’s on Al Kahera Wal Nas. According to him, low-ranking Brothers must pick a side and do so now, otherwise he’ll be forced to categorize them with their leaders and treat them accordingly. He also took care to note that the revolution was made for freedom, justice and success, and only that. The “MB hates the first two,” he said, and failed at the third. Therefore, he decreed that no one can chant “Islamic, Islamic” anymore, since he, the revolution personified, just wants that those three things. However, you think the second slogan can achieve the first, then just say the first, he suggested, not unkindly.

Another example would be Eissa’s on-air calculations to work out the cost of the Raba’a sit-in. A minimum of two million Egyptian pounds a day, he said, just to feed and hydrate all of the “don’t have an iPad or iPhone...simple (-minded rural) people,” as Rashwan puts it - who were hailed as the wise true Egyptians when protesting against Mubarak and Morsi, but were instantly reminded of their illiteracy rates the moment some of them sided with Morsi - and, of course, all of Nasr City’s Syrian jihadists.

That two million or more Eissa and many, many others, are certain is coming out of the pockets of one sinisterly rich Brother, who is using food as payment. It can’t be that the all or some protesters are buying their own food, individually or collectively and sharing. That’s not only a naive thought, but it also dangerously implies that the Raba’a protesters are there out of conviction, and not for a meal. At least, not just for a meal.

“Where (is the MB) getting all that money from?” Eissa demanded an answer for what must be the 238th time, but to no avail. 

Interestingly enough, despite the fact that the media people have unanimously agreed that the MB is a terrorist group, only fit to run a supermarket chain, with mindless members, out to radicalize society and abuse religion; almost all of them have recently asked the MB to stick the da’wah and never ever, ever, dabble in politics again. In other words, spread your filth in some mosque in Kafr el-Sheikh, just not the parliament, thank you very much.

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