Friday Fisking: WW and ERVs

Yes, it’s the return of Friday Fisking. My first target is a chap calling himself William Wallace over at ERV. Some time ago, William left a comment in which he expressed skepticism that ERV data is justifiably used to support common descent. About a week later, he announced that he had made a model based on random insertion, and then asked for some help in creating an equivalent common descent model, with an aside that the results of the random model “doesn’t look good for your side.” This announcement was met with great derision, with calls for William to explain his conclusion. I directly addressed his question about his common descent model, pointing out where his assumption was incorrect. Even so, I remained puzzled as to how he achieved the results he claimed for both models.

Recently, it was brought up in relation to another post about ERVs. Although William refused to give any details about his model, he claimed that his results were unsurprising if you understood that math. He eventually offered to give me details via email. After a series of exchanges, I received enough information to be confident about the basics of his model.

Splish, Splash, Draw Me an Extrasolar Bath

With all of the hoopla this week surrounding the announcement of the discovery of Gliese 581e (the smallest exoplanet yet discovered at 1.9 Earth-masses) and the refinement of the orbit of Gliese 581d (placing it firmly in the habitable zone of the Gliese 581 stellar system – meaning it may have liquid water at the surface), I thought I’d offer an engineering perspective. A number of sites have discussed the theoretically possible means of getting there. But what about realistic means of getting there?

We’re Moving!

Quite a few of the blogs I’ve followed have said that, often when joining the SciBorg collective.  No worries!  You won’t have to update any of your links.  Missing The Point isn’t going anywhere any time soon (insert snark here).

I, however, am moving my physical address next month.  For only about $50/mo more (including extra utility costs), I’ll be closer to work (with a more convenient route), closer to a number of friends, closer to my wife’s family, and getting an additional 200 sq.ft. of living space.  The cons: further from my family and further from a number of our friends.

Some of the things I like about the new place:

1. Less square footage lost to hallway, meaning we get an extra bath (shower not tub) and walk-in closet
2. A big pantry in kitchen (no pantry in the old place!) in place of utility room
3. Slightly larger bedrooms, with lots of light (wall-to wall window starting @ 45″ a.f.f.)
4. Better layout of closet shelving (old place had shelving that we could only utilize at 50% capacity)
5. Larger dining room that isn’t a through-fare to living room and dining room
6. Bigger living room – with a gas fireplace!
7. A covered balcony 6 times larger than our current one – and as a result, nearly 3 times the light into the living & dining rooms

Some things I’ll miss about the old place

• Less counter space in kitchen
• Hanging space in closets not as well laid out
• Laundry room now a closet
• Fewer places to hang pictures (or swords or crossbows)

Of course, the real reason we are moving is my wife.  (No, not that!)  She is working on her Ph.D. and the current layout simply is not conducive to her writing her dissertation.  In fact, the current set-up is directly leading to health problems.  So it’s time to cut bait.

Which means that the current molasses-in-January posting rate is going to become positively glacial.  We are going to be moving pretty much all of May.  The good news is I do hope to have a major project for the blog done by early June.  And the new arrangements will also make it more likely that I will have motivation to actually work on the blog.  Motivation, not inspiration, has always been my problem.

For Our Canadian Correspondent

In the comments in the previous post, monado makes a request:

Post something else! It’s April!

If you’re short of inspiration, take your excellent explanation of Hawai’ian certificates of live birth from Ed Brayton’s blog and post that. It was admirably clear.

This of course is in reference to the claims that Obama is not qualified for President.  Specifically, that because Hawai’i issues COLB to certain individuals born outside of Hawai’i, his COLB doesn’t prove that he was born in Hawai’i.  Unfortunately, it looks like my original comment got mangled.  So here’s how it was supposed to look:

IF Obama were a Natural Born Citzen, he would have long ago produced his Birth Certificate (the Certificate of Live Birth is NOT even accepted by Hawaii as proof of Hawaiian Birth )

Incorrect. The reason the short form (COLB) is insufficient for proof of Native Hawai’ian birth is because the short form doesn’t have proof that the parents are Native Hawai’ians. And by Native Hawai’ian, I mean descended from the original, indigenous population, the Hawai’ian equivalent of Native Americans.

For everything but certain genealogical data, the COLB is legally the equivalent of a certified photocopy of the original. That means that a COLB is sufficient proof of citizenship to get a driver’s license, register to vote, get a government job, get a passport, and even become President of the United States of America.

(I also had wanted to respond to Michael Raston in the same post, but that part and the quote from Gregory Black somehow got deleted, and I can’t remember what I said).  A followup to that comment:

wrt COLB for non-Hawai’ian birth:

If the parents of a child born outside of Hawai’i lived in Hawai’i as their primary residence for at least a year before the child was born, they can request a birth certificate issued by Hawai’i. One reason is for the extra information required for the indigenous population program I mentioned earlier. The other reason is more pragmatic: Hawai’i is in the middle of the world’s largest ocean. Although not as difficult as it once was, it’s a major expense for someone to get certified documents if they are not stored on the archipelago. However, as noted, the vault copy and any other copy, such as the short form (often called the COLB, even though the long form acronym also is COLB) by law must have the accurate place of birth.

For similar reasons, adoptive parents may also request a Hawai’ian birth certificate. I am unaware of any provisions for immigration (and would be surprised if there were, because the immigration documents should have the necessary information).

Hope that clarified things.

Caldwell Denied, Caldwell Wins

The most recent Establishment Clause lawsuit presented to the Supreme Court, Caldwell v. Caldwell (no relation), was denied a writ of certiorari by the Court today. The suit was filed by Jeanne Caldwell, wife of the infamous Larry Caldwell (who is known for filing frivolous lawsuits against teaching evolution). The defendant was UC Berkeley (coincidentally, the lead defendant is also named Caldwell), which maintains the Understanding Evolution website. The lawsuit was previously dismissed at the District and Circuit Court levels due to lack of standing. This denial of cert officially ends the lawsuit.

I’ll Have the Mayo, Hold the Reuben

The academic blogosphere is buzzing with the recent discovery of a major incident of academic fraud.  Dr. Scott Reuben published 21 papers over the course of 12 years that have been implicated in the fraud, making this one of the largest cases of academic fraud ever discovered.  Worse yet, Dr. Reuben’s research is in medicine, throwing a primary method of post-surgical treatment into disarray.

Gradualism, Contingency, and Punctuated Equilibria

Since Ed is in Vegas again, I offered to put up some guest posts to help alleviate the terrible burden being placed on him.  And today being Darwin Day, I thought I’d put up a post on evolution.

As a consequence of lacking data supporting their own explanations, creationists, like other denialists, have to rely on attacking perceived weaknesses in the mainstream theories.  A popular target arises whenever disagreements between scientists over aspects of the theory crop up.  These disagreements are then exaggerated so as to makeit seem as if the whole edifice is crumbling, when in reality it is just a minor difference in opinions, both of which can be explained by the theory.

In evolution, one such disagreement is between gradualism and punctuated equilibria.  Broadly speaking, gradualism is the idea that changes accumulate over time, while punctuated equilibria is the idea that there are short periods of lots of change interspersed among long periods of little change.  Since these two ideas appear to be contradictory, creationists love to use the debate over the two concepts as evidence that evolution is wrong.  However, the two concepts are not only not contradictory, under the right circumstances gradualism results in punctuated equilibria.

And Now for Something Completely Different

Let’s take a break from litigation and turn our eyes on ligation. The type of ligation I am talking about is connecting two strands of nucleic acids (RNA in this case; a similar process with the same name takes place with amino acids) to make a longer strand. This is an important concept in origins-of-life research (and in biology), because it allows long strands with high information content to be assembled in shorter segments, kind of like a chemical assembly line. (Note that I am using “information content” in the sense of compressibility). In essence this allows Nature to reduce the odds against producing the right sequence of bases in a long strand. It’s generally much easier to reliably produce short strands than it is to reliably produce long strands.

Of course, it doesn’t do you any good if the shorter strands are simply connecting at random – this doesn’t reduce the probability. So what you want is a process that reliably connects the correct strands in the correct order. The process doesn’t have to be perfect, just better than random. One way to do this is by speeding up the ligation process for the right strands in the right order – in other words, use a catalyst. RNA has an interesting property – it has a “backbone” that strongly connects linearly, as well as matching base pairs that connect weakly. This means that RNA can act as a catalyst for itself – an autocatalyst. Are there combinations of short RNA strands that reliably catalyze into longer strands?

What would be even cooler is if the longer strand could act as a catalyst that takes the short strands and makes another long strand just like itself. That’s self-replication, the first step towards life.

Chemists at the Scripps Research Institute did just that.

No Can Has Cert, Berg

Jan 12 2009  Petition DENIED.

The Supreme Court announced today, in a totally expected move, that they were denying certiorari to Philip Berg’s quixotic attempt to prevent Obama’s ascendancy to the office of President of the United States of America.  This also makes moot this Friday’s hearing on the injunction pending disposition of cert – the cert has been disposed.  Properly.  In the circular file.  Rumors of hysterical laughter emanating from chambers are as yet unsubstantiated.

Vegas Vicarious

I have great news!  I will be guest blogging for Ed Brayton over at Dispatches from the Culture Wars.  Ed is going to Vegas this week – anyone who follows his blog know that he enjoys gambling.  Since he usually posts 5 times a day, he invited several bloggers to  fill in for him.  He pulled together a crack team of bloggers: Radley Balko, Chris Rodda, Jon Rowe, James Hanley, and the infamous DarkSyd, a veritable Who’s Who of legal blogging.  So why me?

He’s a gambler.  It’s no fun going with just the safe bets, eh?

So join me over at Dispatches all week long, and maybe I can kick start my own creative juices.