Archive for the ‘News’ Category

Open wide, let me put this in you

Thu Jan 30, 2014 12:52 am by Prolescum

Given that the UK Government is considering switching to open source formats and software, and that several municipalities (or entire government departments) within and without the EU have decided to ditch proprietary software in favour of FOSS (Free and Open Source Software) alternatives, it’s worth us having a look at the pros and cons of such a move, if only to better understand (or object to) the decisions being made at this level.

Firstly, a quick explanation of the terms are in order:

Open Source Software: See here for the official Open source Definition

Open source is a development model based upon the “four software freedoms” elucidated by Richard Stallman of the Free Software Foundation as: the freedom to run [the] software for any purpose; the freedom to study how the program works and change it to suit your needs; the freedom to redistribute the code; the freedom to distribute your modified software so others may benefit from your changes.
The free in Free Software refers to liberty, not price. In practice, this means that using software with an open source license gives developers, engineers and end-users the ability to share their ideas and make contributions (fix errors or bugs, add new features etc) that benefit anybody using said software. It also means that the code is available for constant review, giving rise to the argument that FOSS deals easily and promptly with, for example, security issues.

Proprietary Software:

Software licensed under the exclusive terms supplied by the copyright holder. Generally speaking, proprietary licenses give the right only to use the software under certain conditions, in practice meaning that one is restricted from modifying, sharing, studying, distributing or reverse engineering the code.
Only the provider of the software has access to the source code, and therefore only they can modify, release updates or add new functionality to the software.


It’s worth noting that both proprietary and open source (or free) licensing uses the same legal basis (usually copyrights) to construct agreements. Proprietary licensing (most often in the form of an End User License Agreement) will state precisely what you can and cannot do with your purchased license, whereas open source licenses can vary from completely free, i.e. no restrictions at all, to the requirement that published code must be released using the same or equivalent licensing.

So how would it benefit government departments?

1. Switching formats (for example from Microsoft’s proprietary .doc Word document format to the open standard .odt format) could mean that all government departments regardless of operating system or software in use will be able to read and write to the same target and expect the same results. Of course, I suspect this happens now with office documents, but is burdened by an EULA with an annual fee.
As the format has new features added, no additional cost is applied outside the manpower required to roll out the updates. This would also make it easier for the various departments to deploy a variety of operating systems depending on their needs without the burden of having to re-format documents for particular users.

2. Overall costs of deployment are reduced (not paying for licenses or new iterations of the software, for example). This is a disputed one, as a counter argument exists. The cost of retraining staff for using new software, and the cost of training or employment of new IT staff with a new system has been said to vacuum up any savings made by switching.
As it currently stands, much of the UK Government is still using versions of Windows and other related software created well over a decade ago, so I believe the retraining costs of switching would amount to much the same were they to update to more modern versions, with the added benefit of lower future spending.

3. Updates, bug fixes, plugins and tweaks etc can be created in-house without additional licensing or approval. Most IT departments, whether government or business, have employees who write and deploy software for front- or back-end offices. An easily understood example might be an intranet where employees have access to FAQs, forums, customer databases and the like. As has been my experience, certain parts of an intranet may make use of bespoke Internet Explorer (Microsoft’s default browser) features, such as ActiveX plugins. Only IE supports ActiveX, and only Microsoft decides whether a plugin is still useful or will be deprecated.
This is a problem because the choices are often either to use an outdated browser (not secure when used outside the intranet) or rewrite from scratch to whichever iteration they update to. This is a vicious circle, and would be ameliorated by using an open standard such as HTML5 to code the intranet and open source software to maintain legacy features (for example by using a browser’s plugin architecture or altering its code) while keeping up-to-date with regards to general internet security.

4. Writing your own software. Libraries and back-end services written for one open source program can often be used in other programs without express permission (depending on the license), lessening the burden of writing new ones from scratch.

What are the downsides to switching?

1. With regards to format-switching, Microsoft Office now supports open document formats, so only some brief training informing staff to save in .odt would be required. Switching entire platforms may require further training due to the variety of options available outside the proprietary software pool, however, given that various departments may be required to give training for new versions of proprietary OS deployments, I believe the costs are comparable.

2. Long term viability. An issue that comes up within the Open Source communities is what to do with a project when its creators or maintainers decide to no longer support the software. This could add to the overall costs if a department depends on some code that is no longer supported, as it may require a switch to an alternative or for the IT chaps to maintain it themselves.

3. Interoperability. An issue that plagues the modern world as a whole, really, but one that should concern a government considering deployment of FOSS. An example might be using Microsoft’s Exchange for email. Support for ActiveSync et al outside the Windows environment is choppy, if not appalling.

4. Regulations. There may be legal requirements upon software deployment, such as using particular encryption methods or in fact using software with specific licensing restrictions, exemptions, or requirements. I believe this would be the issue most necessary to adhere to, and the most difficult to overcome.

All cards on the table, I am an advocate of FOSS, so my opinions should be regarded accordingly.

That said, these are only a few of the pros and cons we should consider (the ones that came to mind when writing this post…). Can you think of any other issues governments could run into from a switch? Or perhaps you’ve noticed a benefit not noted above? How about a mistake I’ve made? Comments and suggestions very welcome through the comments link below.

Further reading:

List of Open Source Licenses
Legal Issues and Best Practices around procuring or deploying open source software

Another ridiculous poll from the Daily Express.

Sun Nov 03, 2013 10:31 am by theyounghistorian77

According to probably the UK’s most hyperbolic newspaper on a front page published on November 1 2013, “98%” of respondents to its survey agreed with a motion that there should be a “crusade” against migrants, particularly Bulgarian and Romanian ones. A classic argumentum ad populum.   Of course what the daily express did in setting the question was to contextually load it by embedding it within a stream of highly negative information about the subject matter. The previous day, for example, the Express ran a story suggesting within it that 28 Million (emphasis on that number) Romanians and Bulgarians could be coming to our shores. Any astute observer of population statistics would immediately pick up that “28 Million” is a cumulative figure representing both the approximate populations of Romania (appx 22 Million rounded) and Bulgaria (appx 7 Million rounded) [So actually appx 29 Million, using 2012 statistics]. To suggest that all 28 or 29 Million would indeed be coming here is evidently absurd, for it would mean that there would be absolutely no Romanians and Bulgarians in, erm, Romania and Bulgaria. So why the such large number? 1) Again, tabloid sensationalism 2) Again, negative information. So that figure of 98% agreeing with the loaded question is to be sadly expected, plus the fact that only Express readers were polled anyway. If there should be a campaign against anything, it would be against conducting ridiculously biased polls like this. Of course, not that this is new to the Express anyway. Also, why the image on the front page of what appears to be an Islamic headscarf seeing that Bulgarians and Romanians are overwhelmingly Christian?

Bad times bring us together

Sat Jun 22, 2013 8:17 pm by Inferno

I’m sure most people will have heard of the protests in Turkey. A friend of mine is Turkish so I always get updates, however reliable they might be, through her.

A recent message on her FB recently said the following:

Sehr geehrter Herr Ministerpräsident; heute hast du uns einen Gefallen getan, dessen du dir noch nicht bewusst bist.

Ich habe heute einen Fenerbahce Fan gesehen, der vor den Polizisten, denen du den Befehl zum Angriff gegeben hast, zu Boden gestürzt ist und dem – von einem Galatasaray Fan – auf die Beine geholfen wurde. Schüler, die ihr Brot und Wasser teilen, kurdisch- und türkischstämmige Menschen, die Hand in Hand laufen. Das habe ich heute gesehen.

Frauen, die Sie als Prostituierte bezeichnen sind mit Milch und Zitrone in der Hand, aus den Bordellen, den Verletzten zur Hilfe geeilt. Ich habe gesehen, dass Menschen, die Sie als Travestien bezeichnen, ihre Hotelzimmer für Menschen geöffnet haben, die Zuflucht suchen, Ärzte und Rechtanwälte haben ihre Telefonnummern mitgeteilt, Medizinstudenten haben Erste Hilfe geleistet.

Ich habe ältere Frauen gesehen, die Essigtücher verteilen. Händler, die ihre Netzwerksicherheitsschlüssel freigeben, Hotelbesitzer, die die Verletzten in ihre Lobby nehmen.
Das habe ich heute gesehen.

Ich habe gesehen, dass ein Fahrer der Gemeinde die Straße mit seinem Bus versperrt hat, damit ja kein Panzer eindringen kann. Apotheker, die ihre Apotheken in der Nacht öffnen habe ich gesehen.

Und sei dir sicher, heute Nacht waren nicht die Gasbomben der Grund für die Tränen in unseren Augen – es war unser Stolz !!


That’s quite the wall of text and in German too. Here’s a google-translated version with some corrections on my part:

Dear Mr. Prime Minister, today you have done us a favour, which you are not aware of yet.

Today I have seen a Fenerbahce fan who was thrown to the ground by the police, whom you have given the order to attack on the ground and said fan was raised to his feet by a Galatasaray fan. Students who share their bread and water, Kurdish and Turkish-born people who run hand in hand. I’ve seen it today.

Women who you call a prostitute with milk and lemon in hand, from the brothels, rushed to help the injured. I saw that the people you refer to as travesties, opened their hotel rooms for people seeking refuge, doctors and lawyers have posted their phone numbers, medical students have given first aid.

I have seen older women who spread vinegar cloths. Traders who share their network security key, hotel owners who take the injured in their lobby.
I’ve seen it today.

I have seen that a driver of the municipality has blocked the road with his bus, so it can not be penetrated by armour. Pharmacists who open their pharmacies in the night, I’ve seen it.

And rest assured, tonight it weren’t the gas bombs which were the reason for the tears in our eyes – it was our pride!


In itself, that’s a very nice letter sent to Mr Erdogan by Mr Akyut G.

What stands out though, at least to me, is the sharp contrast between “normal” times and “problematic” times. Generally, the football (and by that I mean soccer) fans would beat each other to a bloody pulp. The prostitutes would be shunned by large parts of the society, only to be required later on.

I don’t think this is at all unusual. For example, Germany was heavily shelled in WW2 (and in turned shelled others quite severely) but when a common enemy, the Soviet Union, was declared, other Western powers fairly quickly allied themselves with the Germans.

Yet as soon as this common enemy faded away, nationalist feelings would tend to grow and allies would once again become… well, not quite enemies, but relationships faded.

I’ll draw on one example to explain what I mean: In a recent blog post about right wing parties I introduced the Austrian party FPÖ. They’re probably the most right-wing party you can currently find in Austria. Looking at the results of national votes in Austria one can see a curious trend: With very few exceptions, the FPÖ had fewer than 10% in most counties, but in 1988, just as the fall of the Berlin Wall was imminent (as we now know in hindsight), the FPÖ suddenly made a tremendous jump in votes. (In some counties earlier, see Oberösterreich, in some a bit later)

Now there might be any number of reasons for that, but I’ll only focus on the two main reasons: In 1986, Jörg Haider took over the FPÖ, which may have caused votes to soar.
I don’t think so, however. If he were the reason for the jump, you’d have expected votes to go down after he split from the party in 2004 and after he died in 2008. The opposite is true: Though a slight dip can be seen in 2004 (after Haider created the BZÖ, the second right-wing party in Austria), the numbers rose again a few years later and the total right-wing voters consistently rose.


This leaves, in my opinion, only one conclusion, which incidentally is the second reason I said I’d mention above: Nationalism, at least in Austria, is on the rise. I think the same holds true for many other countries: The Front National (FN) in France has constantly gained votes in the presidential run since its inception in 1974. Both the Nieuw-Vlaamse Alantie (NV-A) and the Vlaams Belang (VB) have gained votes and would currently hold over 50% if they worked together. Even the British National Party (BNP), by the way the only party that Wikipedia claims is “right-wing extremist”, has gained votes, even though they currently barely reach 2%.

I think the trend is clear: Nationalism. right-wing tendencies and euro-scepticism is on the rise and with it a sort of “fight for yourself” attitude. I think that’s all fairly undeniable.

There are two questions I would like to pose:

1) What can be done to counter that movement? It seems a fair number of people who would have voted centre-right are now voting left, simply because they’re frightened by a right-wing takeover or a cooperation. (Lefties would never work with right-wingers… right?)

2) Seeing the post in the context of the above letter: Do you think it’s true that we will only fight side by side if there are common enemies, as opposed to common goals? I can’t shake the horrible feeling that there might be something to it.

The ENCODE delusion

Sun Apr 07, 2013 6:10 pm by Inferno

A few months ago, I wrote a post about junk DNA and ENCODE. Since then, more evidence has surfaced so I’ve decided to make this into a blog post. I’ve slightly modified the original post as well as added the new information plus all the relevant links. This is a long and sometimes technical post. Note: “Creationist” is interchangeable with ID-proponent. They’re the same.


The main problem with this story is not what scientists have claimed and then found, but rather what the popular press has (mis)understood. This is also a story about scientists failing to communicate science properly. AronRa said on the 31st of May, 2009, in his video Ida Know (the first of a five-part summary about the 47-million year old primate fossil Ida) the following, which also holds true about this story:

But sadly, the media isn’t entirely to blame, some of this has been done by scientists.

It is highly inappropriate sensationalism and the way it’s described is very misleading to anybody who doesn’t understand taxonomy very well and almost nobody does.

The same is true in this case, only substitute “taxonomy” with “evolution”, “genetics” and “biochemistry”.
A pop-science journal Arstechnica (Author John Timmer) has also commented on this phenomenon:

ArsTechnica: Most of what you read was wrong: how press releases rewrote scientific history

Many press reports that resulted [from the ENCODE release] painted an entirely fictitious history of biology’s past, along with a misleading picture of its present. As a result, the public that relied on those press reports now has a completely mistaken view of our current state of knowledge (this happens to be the exact opposite of what journalism is intended to accomplish). But you can’t entirely blame the press in this case. They were egged on by the journals and university press offices that promoted the work,and, in some cases, the scientists themselves.

Unfortunately, things like well-established facts make for a lousy story. So instead, the press has often turned to myths, aided and abetted by the university press offices and scientists that should have been helping to make sure they produced an accurate story.

I’ll go into the details of the ENCODE story near the end, but first we need a short history of “Junk DNA”.

A history of “junk DNA”

The story begins with Susumu Ohno. In 1970, he wrote a book (Ohno, 1970a ) in which he laid out the argument for the role of gene duplication in evolution. We now know that it does indeed play its part. One thought experiment he had regarded genes that were duplicated (in his example, three sequences sharing the same sequence) and not under pressure by selection any more. If there is no selective pressure, they would mutate and two out of three would likely serve no function, due to high mutation rates.

Ohno 1970a, p.62

[It is likely that] in a relatively short time, two of the three duplicates would join the ranks of ‘garbage DNA’.

This was the first time anything like this was proposed. Only two years later, in another paper (Ohno, 1972) would he coin the phrase “junk DNA”. So what was “junk DNA” or “garbage DNA” to him? Well it’s based on a very well-known observation:

Ohno 1972

If we take the simplistic assumption that the number of genes contained is proportional to the genome size, we would have to conclude that 3 million or so genes are contained in our genome. The falseness of such an assumption becomes clear when we realize that the genome of the lowly lungfish and salamanders can be 36 times greater than our own.

As we now know, we have roughly 20,000 genes, which fit well with Ohno’s prediction of no more than 30,000 genes. It was also observed that there can be a lot of duplications and insertion of retroposons without affecting the body in any way. I talk about this later on, under the heading “pseudogenes”.

At the time of Ohno’s writing, “junk DNA” was “meant to describe the loss of protein-coding function by deactivated gene duplicates, which in turn were believed to constitute the bulk of eukaryotic genomes”. (Genomicron, 2007)

A very important part follows:

As different types of non-coding DNA were identified, the concept of gene duplication as their source, and therefore “junk DNA” as their descriptor, found new and broader application. However, it is now clear that most non-coding DNA is not produced by this mechanism, and is therefore not accurately described as “junk” in the original sense.

So in the original sense, we don’t have a lot of “junk DNA” after all. The important thing to know here is that the term has been butchered by the media to mean all non-coding DNA, which strictly shouldn’t be called “junk DNA” but rather “pseudogene”, coined in 1977 (Jacq et al. 1977) to describe a functionless gene. Now note the miscommunication: There is a difference between “junk” (stuff one keeps) and “trash” (stuff one throws out). This was noted in 1988:

Brenner 1998

There is the rubbish we keep, which is junk, and the rubbish we throw away, which is garbage.

And in 1990, Brenner said the following:

(S. Brenner, The human genome: the nature of the enterprise (in: Human Genetic Information: Science, Law and Ethics, No. 149: Science, Law and Ethics, Symposium Proceedings (CIBA Foundation Symposia) John Wiley and Sons Ltd 1990, Source) <– One problem with that blog post is that much of it is wrong. I merely provide the source to show where I got the picture from.

And even in 1973, Ohno suggested a potential function for “junk DNA”:

Ohno, 1973

The bulk of functionless DNA in the mammalian genome may serve as a damper to give a reasonably long cell generation time (12 hours or so instead of several minutes)


Genomicron, 2007

From the very beginning, the concept of “junk DNA” has implied non-functionality with regards to protein-coding, but left open the question of sequence-independent impacts (perhaps even functions) at the cellular level. “Junk DNA” may now be taken to imply total non-function and is rightly considered problematic for that reason, but no such tacit assumption was present in the term when it was coined.

Gregory goes on to make a very astute observation: If there is no function for all genes, creationists are in serious trouble. (Note: Recent reading of a creationist blog post suggests that there is at least one creationist who does not adhere to this and thinks it wouldn’t matter much if their prediction weren’t true. I’ve yet to find the original source [a guy called Axe?] so I’m left to wonder how that should work… This doesn’t detract from the point that most creationists do hold the view presented both above and below.)

Genomicron, 2007

[This is why] all non-coding DNA must, a priori, be functional.

To satisfy this expectation, creationist authors (borrowing, of course, from the work of molecular biologists, as they do no such research themselves) simply equivocate the various types of non-coding DNA, and mistakenly suggest that functions discovered for a few examples of some types of non-coding sequences indicate functions for all (see Max 2002 for a cogent rebuttal to these creationist confusions). Case in point: a few years ago, much ado was made of Beaton and Cavalier-Smith’s (1999) titular proclamation, based on a survey of cryptomonad nuclear and nucleomorphic genomes, that “eukaryotic non-coding DNA is functional”. The point was evidently lost that the function proposed by Beaton and Cavalier-Smith (1999) was based entirely on coevolutionary interactions between nucleus size and cell size.

Apart from the above mentioned potential function for “junk DNA”, many more have been identified since:

Genomicron, 2007

Examples include buffering against mutations (e.g., Comings 1972; Patrushev and Minkevich 2006) or retroviruses (e.g., Bremmerman 1987) or fluctuations in intracellular solute concentrations (Vinogradov 1998), serving as binding sites for regulatory molecules (Zuckerkandl 1981), facilitating recombination (e.g., Comings 1972; Gall 1981; Comeron 2001), inhibiting recombination (Zuckerkandl and Hennig 1995), influencing gene expression (Britten and Davidson 1969; Georgiev 1969; Nowak 1994; Zuckerkandl and Hennig 1995; Zuckerkandl 1997), increasing evolutionary flexibility (e.g., Britten and Davidson 1969, 1971; Jain 1980; reviewed critically in Doolittle 1982), maintaining chromosome structure and behaviour (e.g., Walker et al. 1969; Yunis and Yasmineh 1971; Bennett 1982; Zuckerkandl and Hennig 1995), coordingating genome function (Shapiro and von Sternberg 2005), and providing multiple copies of genes to be recruited when needed (Roels 1966).

In addition, I believe one can add both Epigenetics and Evo-Devo to that list.

Finally, Genomicron notes the following:

Genomicron, 2007

More broadly, those who would attribute a universal function for non-coding DNA must bear the following in mind: any proposed function for all non-coding DNA must explain why an onion or a grasshopper needs five times more of it than anyone reading this sentence.


Now I need to explain pseudogenes. I think the easiest way is to use this picture from the wikipedia article, which I modified for the purpose of illustration:

As you may know, amino acids are encoded by reading DNA sequences in triplets. If, as in the above sequence, an insertion, deletion and point mutation occurs, the triplets are read differently. The results in amino acid encoding are shown above. If the new sequences produce premature stop-codons or, as in this case, simply different amino acids, genes may not be activated and proteins may not be produced. Sometimes they are encoded but do not actively help the organism.
These are then called pseudogenes.

The ENCODE delusion

A few months ago, the ENCODE staff published some research, which prompted the following statement by the EFF:


On September 19, the Ninth Circuit is set to hear new arguments in Haskell v. Harris, a case challenging California’s warrantless DNA collection program. Today EFF asked the court to consider ground-breaking new research that confirms for the first time that over 80% of our DNA that was once thought to have no function, actually plays a critical role in controlling how our cells, tissue and organs behave.

But as I showed above, functions for “junk DNA” have been known since before the term was even coined! This is what I’m talking about when criticizing the way scientists convey science and the way newspapers bring it to the public. (Luckily, some scientists have spoken out against the ENCODE fiasco. And hey, even some folk from the ID-crowd.)

But let’s back up a little. ENCODE has been working for quite some time now and, as you would expect, it has been talked about since at least 2007. (Arthur Hunt on Panda’s Thumb, 2007) Even then, Creationists wanted to claim what they claim now, namely that all DNA has a definite function. There was (at least) one problem for them: A 2005 paper (Wyers et al. 2005) showed that “much of the RNA made by a cell is thrown away. This includes RNA encoded by intergenic regions.” (Quote from Arthur Hunt, 2007)

PZ Myers documents a second story, with a 2010 paper (van Bakel et al. 2010) explaining once again that genes only make up about 2% of the genome, while the rest is non-coding.

That takes us back to the 2012 report from ENCODE. They claimed that 80% of the genome serves some biochemical function, with “function” being defined as participating “in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type”. That’s where the real problem in communication lies: The definition of the word “function”.

PZ Myers

That isn’t function. That isn’t even close. And it’s a million light years away from “a critical role in controlling how our cells, tissue and organs behave”. All that says is that any one bit of DNA is going to have something bound to it at some point in some cell in the human body, or may even be transcribed. This isn’t just a loose and liberal definition of “function”, it’s an utterly useless one.

I’ll try to make this as clear as possible, so I’ll draw on an analogy. Imagine you found two ball-point pens. One of them is a normal pen, the other lacks the ball-point. The first pen has a definite function: To write. The second one may have other functions (like removing ear-wax from your ear), but that’s not a definition of function any sane person would recognize.
The same happened to ENCODE: The way they define “function” is so broad that it’s absolutely useless. Indeed, much randomly generated DNA can be said to have “function” under this definition.

Also note that in his blog, Ewan Birney (kind of) explains what “function” means in ENCODE terms. What’s noticeable is that it could just as well have been swapped for “specific biochemical activity”, which takes the wind out of the sails completely.
In another Q&A point, he said that using the 80% number instead of the 20% functional bases (notice a difference?) was used to… hype up the story. That’s basically it.

Ewan Birney, Q&A

Q. Ok, fair enough. But are you most comfortable with the 10% to 20% figure for the hard-core functional bases? Why emphasize the 80% figure in the abstract and press release?
A. (Sigh.) Indeed. Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader, they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to “4 million switches”, and that represents the bound motifs and footprints.

We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity.

And again from Arstechnica:

So even as the [2007] paper was released, we already knew the ENCODE definition of “functional impact” was, at best, broad to the point of being meaningless. At worst, it was actively misleading.

In the lead paper of a series of 30 released this week, the ENCODE team decided to redefine “functional.” Instead of RNA, its new definition was more DNA focused, and included sequences that display “a reproducible biochemical signature (for example, protein binding, or a specific chromatin structure).” In other words, if a protein sticks there or the DNA isn’t packaged too tightly to be used, then it was functional.

That definition nicely encompasses the valuable regulatory DNA, which controls nearby genes through the proteins that stick to it. But,and this is critical,it also encompasses junk DNA. Viruses and transposons have regulatory DNA to ensure they’re active; genes can pick up mutations in their coding sequence that leave their regulatory DNA intact. In short, junk DNA would be expected to include some regulatory DNA, and thus appear functional by ENCODE’s definition.

The ENCODE team itself bears a particular responsibility here. The scientists themselves should have known what the most critical part of the story was,the definition of “functional” and all the nuance and caveats involved in that,and made sure the press officers understood it. Those press officers knew they would play a key role in shaping the resulting coverage, and should have made sure they got this right. The team has now failed to do this twice.

All that being said, Sandwalk notes two things:

1) The word the ENCODE-people are looking for is not “function”, it’s “noise“.

2) The debate isn’t only about the definition of “function”, but something deeper. An additional problem may be that some scientists don’t understand evolution. That’s pretty sad in this day and age.


A further update comes from a 2013 paper in “Genome Biology and Evolution”. The paper is discussed over at Pharyngula and it basically rips into ENCODE’s papers. There’s a lot of technical stuff I needn’t cover, so I’ll limit myself to mentioning one thing: Other researchers have found only 10% true functionality, that’s 70% less than the folk over at ENCODE.

I’ll conclude:

1) “Junk” DNA was, from the moment of its conception, a misnomer. Just like “Big Bang” falsely conjures the image of an explosion, “junk DNA” falsely conjures the image of complete non-function or garbage. However, in both cases that’s not consistent with what scientists have been saying even before the term was coined. “Junk DNA” should not be in common usage. A more precise term would be “pseudogene”.

2) Conveying what “junk DNA”, non-coding DNA and pseudogenes are, as well as the nuanced differences between the terms, is a difficult job. Sadly, neither scientists nor journalists have done a good job of explaining the terms. It would be interesting to make an extremely careful and detailed YT series on this subject.

3) Much of the ENCODE hype rests on the definition of the term “function”. If the general public and creationists were aware of what “function” means in ENCODE terms, the hype would almost completely fade away. Note that I’m not saying that the results were wrong, inconclusive or not worthy of recognition, I’m simply saying that they were over-hyped. (Which would put them into the second circle of scientific hell!)

4) This problem also creates an opportunity. We now understand what we did wrong and this may encourage scientists to be more careful in the future when explaining things. I hope to make a blog series on the public understanding of science soon and this will be one of my focuses.

Below are all the references used in the creation of this post. The first one is only scientific papers, the second one is blog posts and opinion pieces.
All references with links attached are the resources I used myself, other resources in plain black are additional resources.


Andolfatto, P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.

Batten, D. 1998. ‘Junk’ DNA (again). Creation Ex Nihilo Technical Journal 12: 5.

Beaton, M.J. and T. Cavalier-Smith. 1999. Eukaryotic non-coding DNA is functional: evidence from the differential scaling of cryptomonad genomes. Proceedings of the Royal Society of London, Series B 266: 2053-2059.

Bejerano, G., M. Pheasant, I. Makunin, S. Stephen, W.J. Kent, J.S. Mattick, and D. Haussler. 2004. Ultraconserved elements in the human genome. Science 304: 1321-1325.

Bennett, M.D. 1982. Nucleotypic basis of the spatial ordering of chromosomes in eukaryotes and the implications of the order for genome evolution and phenotypic variation. In Genome Evolution (eds. G.A. Dover and R.B. Flavell), pp. 239-261. Academic Press, New York.

Bergman, J. 2001. The functions of introns: from junk DNA to designed DNA. Perspectives on Science and Christian Faith 53: 170-178.

Biémont, C. and C. Vieira. 2006. Junk DNA as an evolutionary force. Nature 443: 521-524.

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References from pop-science resources

Gregory, T. R. 2007. Genomicron Junk DNA summary

Genomicron ENCODE reply

Brenner, S. 1998. Refuge of spandrels. Current Biology 8: R669.

Talk Origins summary

Talk Origins claim CB 130

Pandas Thum: Junk DNA

Possibly slightly misleading article at ScientificAmerican on Junk DNA <— Read this one only after you’ve read the other ones plus my summary, otherwise you might be a bit confused!

Sandwalk has many more articles on the topic. They’re not a must-read, though, merely more information on the same.

Findandpea have another great review of the way the media failed to report properly on this. But again, scientists fell for it too, so reporters are not exclusively to blame.

Finally, Genomicron maintains an updated list of posts on the topic over at his blog. In case you’re missing anything, it can either be found at Sandwalk or at Genomicron.

Habemus Papam! And what do believers say?

Fri Mar 15, 2013 10:58 pm by Inferno

A new Pope has been elected. I won’t comment on the choice, it’s obviously the outcome of an internal political struggle and a need to show that people outside of Europe are represented in some way or other. Note that the Pope is still white, so no thought was given to true multiculturalism. It may even be considered that he only grew up in Argentina, but because his parents were Italian he can’t be said to be South American with a straight face. It’s been said that this Pope, just like the last one, will result in a decline in followers and possibly even help speed along atheism, but while the former is almost certainly true the latter is up for debate.

That all of this clashes with the idea that God elects the Pope is glaringly obvious, but I’ll skip all of that and focus on something else entirely: What are the responses by believers to the new Pope?

To look at that, I’ll pick some comments from FB, twitter or newspapers and check what people are saying.
The choice of comments is not representative and merely reflects the biases of the author.


The first comment comes from one of my friends, posted on FB. The English translation reads:

Francesco I. from Buenos Aires. A good choice. A good prayer.

How this guy knows that it was a good choice is a mystery to me. Others have already complained that this Pope was a bad choice, being a homophobe, conservative, anti-progressive kook. It also once again calls into question what any of this choosing has to do with God’s will. If God were choosing, we’d have a Pope in the first few minutes by unanimous vote but NO!, it sometimes takes ages to elect a new one.

The second thing is the “A good prayer” bit. It can be understood in two ways, one of them is entirely bizarre.
1) After seeing that a new pope was elected, said friend prayed and felt good about it. Slightly weird, but not bizarre.
2) He or someone else prayed for the outcome to be what it is or prayed for a good outcome. The second bit is subjective, so I’ll address the first. If that really were the case, why did God answer those prayers and not the other ones? What happens to God’s will if he has to bow down to your prayer?


The second comment can be found here at HuffPo:

Just a matter of time before all the criticism and nasty comments show up before the man has a chance. Pope Francis’ religous beliefs and convictions belong to him. He doesn’t have to justify those beliefs. You may not agree with his beliefs. At least acknowledge that he too is entitled to free speech. We keep getting away from that. Live and let live. No one should be bound and gagged because they reject abortion, reject same sex marriage and reject life styles. As long as that person is civil towards fellow mankind….why, why do others condemn? I don’t agree with abortion. I don’t agree with same sex marriage. This doesn’t mean I don’t love others. I simply do not agree…what is so bad about that? OK…I’m ready for all the ugly feedback. :)

I find it strange that a Pope’s religious beliefs belong only to him. Isn’t he supposed to guide his sheep in their faith-struggle? Even worse, isn’t he supposed to uphold the views presented in the Bible? (He is upholding the whole “no gays” part, so that’s not what I’m complaining about. I’m complaining about the commenter’s views that he can have other views.)

The second part about not “binding and gagging” people because they reject “… life styles” is a wicked idea. People who condemn others because of personal choices that do not harm others (i.e. homosexuality, etc.) is despicable and should not be tolerated in anyone, even less so in people who present a business or a group of people. People get fired about such comments every day, but the Pope is applauded for them. We live in a weird world.

Many other posts are either along the lines of

He was the best we could hope for. Thank GOD

or rationalisations of both his crimes and the crimes of his predecessors.

All of this should lead to some kind of point, right?
Well, going through about 500 comments or so on the BBC, NY-Times, HuffPo, Guardian and some Austrian newspapers’ sites, I noticed three things:

1) There are more people critical of the new pope than there are people endorsing him. It seems that even Christians are aware that he may not have been the best choice.

2) The ones who do protect the pope are very often ignoring large parts of his history. The few who acknowledge that he did some evil things in his past sweep that under the rug and claim that this has no effect on his current stance.

3) Christians who did neither of those, that is to say neither endorse in a weird way nor reject him, post things that are supremely weird.

This post was just a short insight into the weirdness of “moderate” and “enlightened” Christians. Nothing will follow.
I do have one question though: How long do you think it will take before the new Pope says something really stupid? And I’m not talking about the statements issued a few hours after his election á la “homosexuality is bad”, I’m talking “AIDS is bad, but not as bad as condoms”-stupid.

My guess? Before summer.

US Healthcare, Taxes, and the 99%.

Fri Sep 14, 2012 10:30 pm by Dean

As you can see from the title of this essay, I will be writing here on a matter of some importance, regarding the current climate of US politics which will connect to the recent events concerning Paul Ryan’s nomination by the Republican Party to run for Vice-President of the United States. And also, a rebuttal to some common arguments often made in his defense, as I understand them, because of course, many such people exist. I invite those members of the League of Reason forum who are from (living in) the United States in particular, to give me some feedback on this topic.

See here:

Indeed, it’s relatively well understood that Republican candidates of various sorts have somewhat of a history of backing ethically and/or logically indefensible positions, and it seems from a cursory scan of his views and proposed policies (I am unsure if I comprehensive catalogue of his and Romney’s views is available) that a vote for Ryan&Romney will result in a rather alarming series of (likely stupid) policy-decisions, namely: anti-social-welfare, so-called “cut-throat”-capitalism, plutocracy, and (perhaps) legislated religious instruction of some manner, though let’s hope not…

Perhaps his economic stance is not all that surprising, when he is apparently an apologist of Ayn Rand‘s political philosophies:

“‘Public welfare’ is the welfare of those who do not earn it; those who do, are entitled to no welfare.” Ayn Rand (in Atlas Shrugged, 1957)

Economics aside, on the social front, he has also stated that “[He] believes ending a pregnancy should be illegal even when it results from rape or incest, or endangers a woman’s health. He was a cosponsor of the Sanctity of Human Life Act, a federal bill defining fertilized eggs as human beings, which, if passed, would criminalize some forms of birth control and in vitro fertilization.”
And this is just the one the one issue that immediately springs to my mind. Not to mention his views on drugs, gay-rights, and climate change, among other things, and I doubt that he accepts the theory of evolution, somehow, and it seems likely that all of these views are going to affect his policies in some way or another.

And while I realise that Obama has shown himself to be rather inept when it comes to economic issues in general, I haven’t seen any solid evidence that either Ryan or Romney are a significant improvement, and his “published plan” is risible indeed. I don’t believe (as he clearly does, and as a great many of his supporters do); that Obama’s actions are slowing economic prosperity. Because for a start, the most atrocious drop in credit over the last 70-80 years or so will take (likely) years yet for everyone in the United States to creep out of, and that would include almost everyone who makes some impact, e.g. home-owners, consumers (obviously), big and small business entities alike, and of course banks, etc. And with the developments in e.g. housing, I can almost guarantee that consumer-demand will improve. Owing to increased equity that buyers and sellers will use for improvements and suchlike. At this stage it’s hard to tell what will happen exactly.

Obama’s … populist ideologues (or seemingly so); have caused quite a lot of controversy in recent months, and are likely to last until November, but of course, when someone complains about this, it’s worth reminding them that in a first-world democracy such as the United States, the governing body of the state is (at least in principle); supposed to respond fairly to the needs of the population, if that makes adequate sense. And this is where the 99 per-cent come in, though bear in mind that I am referring to the “really existing” 99 per-cent, not the politically fanatical so-called “99 per-cent”.

First, I would like to start a serious discussion of taxes; which may then be continued in the Blog of Reason comments-section; for those of you who have chosen to read this far in, and are interested. And of course this is because the issue of taxation has become a somewhat urgent issue of late, especially in the campaigns. I have some distant family living in the eastern United States, who I have been in communication with via the internet for a significant number of weeks, regarding this topic, as I was curious at the time, and they gave me some much needed information. Suppose, for example, you earn between $6,000 and $7,000 per year, on a net of (for the purposes of argument, again); $25,000  amounting to approximately 26% federal tax rate. As far as I am aware (correct me if I am wrong on this): Mitt Romney’s effective tax-rate was 15%.

Though I should add: workers who are self-employed of which there are a great many get to take that 15 per-cent anyway, meaning a horrid obstruction to any potential job-makers who isn’t already in the “Tea Party” mindset, as many of the US Republicans are. The evidence all seems to point to the fact that the smaller and less recognised business-entities take on markedly more workers than any other business-category (or group) does; yet the majority of the tax-burden tends to be bestowed upon individual operators with little to no available capital to contribute.

To say nothing of this being grotesquely unfair (not to mention profoundly stupid, and anti-competitive) it seems flagrantly obvious that the Democrats (flawed as their own policies may be at present in many regards); do have a valid point when they speak of these disparities, and the fact that huge businesses have succeeded in almost completely externalising the costs of maintaining the infrastructure on which their financial survival depends, to the poor and the workers. Specifically, people who don’t have obscenely expensive legal and accountancy departments to help them horde their earnings (capital) after having already effectively circumnavigated income-taxes on capital-gains as almost all distinguished Republicans tend to do. And still I wonder if Romney & Ryan’s visions of so-called “business-amicable” tax codes work as a means of increasing the rate of productive investment? Merely type “Reaganomics” into any search-engine, so that you can see what I mean.

An equitable and evenly distributed tax-burden (“pay your fair share” encapsulates this theory, I feel), would not be inherently anti-business. It would be sound, fair, and logical. I must stress that the issue is not about being anti-corporation, or anti[/i[-big-businesses. It’s about being pro-fairness. What’s more, is that criticising Obama for not having a jobs-plan as many have done, and as Paul Ryan’s superior (Romney) has done is nonsense too! After all; we could critique possible [i]flaws in his plan, but one does in fact exist, as the above-linked article points out.

“In his news conference, Romney emphasized four ideas in his plan: expanding domestic energy production, working out trade agreements with Latin America, cracking down on China and cutting the corporate tax rate. These are all reasonable ideas. But working out trade agreements takes a long time. Getting the Keystone oil pipeline up and running takes a long time. Rewriting and implementing a new corporate tax code takes a long time. Changing China’s policies takes a long time. It’s difficult to see how any of these ideas creates a substantial number of jobs quickly.

Obama also tends to emphasize four parts of his plan: increasing infrastructure investment, hiring more state and local workers, doubling the size of the payroll tax cut and adding a new set of tax cuts for small businesses and companies that hire new employees. Two of those policies imply directly hiring hundreds of thousands of workers. The other two move money into the economy immediately. It’s easier to see how these policies lead to more jobs and demand in the short term.

In terms of the deficit, the Obama administration has put forward a specific set of ideas mostly by eliminating itemized deductions for wealthier Americans to pay for its plan. The Romney campaign has not yet said how it will cut corporate and individual tax rates without increasing the deficit.

In a sense, what’s really interesting about the Romney and Obama plans is that they don’t conflict with one another. Obama has a set of ideas for boosting job creation now. Romney has a set of ideas for long-term economic growth. You could implement all of Obama’s 41 bullet points and all of Romney’s 59 bullet points simultaneously. There’s nothing about increasing infrastructure investment that keeps you from cutting corporate taxes, for instance.”


Also this:

“Paul Ryan has been a fan of sequestration for his entire career in the House. He has repeatedly called for discretionary spending caps backed by a sequester. On August 1, 2011, he got what he has always wanted. Now that the sequestration might actually take place he says it’s “not good government.””

And this….

… And so forth.

Now onto the issue of medical costs:
Net cost relative to the true medical expense(s) should remain relatively stable for the foreseeable future at least, from much of the evidence that I’ve seen. At least, the overall expense of the health-insurance system in place should go down. I’ll bet that in order to get good employees, businesses are off-setting the lack of insurance with higher wages in at least some cases, in all probability. And while it is indeed mostly accurate, that the ACA requires additional coverage(s) for various reasons, remember that kids (or their parents) will have to pay into the system to get coverage for them or the kids, and apparently the point of that was (1) so that these same people would not go uninsured, and/or (2) such that they make few withdraws on the healthcare system, which was supposed to remunerate costs for insurers!

It is equally accurate that insurance-industry/industries’ (over)reaction to ACA was (or is) also a large contributing factor. Yes, there is a real market uncertainty, and insurers need to insure themselves against that (ha!). But the increase in insurance-provider(s)’ profits since the passage of PPACA have been breathtaking, even as insurers themselves have caused or increased deductibles and cut-payouts, etc. That’s what they call a “parlay”, as far as I know…. hmm…

In fact the covering of…25 or 26 year-olds for example, is obviously going to cost something. The ACA requires them to be on a plan, but doesn’t force their parents to take them. So the end-bearer of the decision will have to be made amongst families themselves … as with most things in the “science” of economics, estimates fluctuate somewhat wildly depending on which numbers you trust, but here’s one that puts it at 2.5 “M” (million). What complicates matters is also the fact that existing conditions are enormous by comparison. Here for example, a Forbes contributor claims that… err… “adult-children” (?) inclusion causes merely 1-3% increases in premiums.

When it comes to government’s role in controlling large sectors of the economy, it’s worth keeping in mind that insurance, at least as it is in the US, is rather like a banking entity. You can only seem to find a loan (insurance) when you don’t need it (or access to much medical care) and unfettered, unregulated capitalism of the kind supported by Republicans like Mitt Romney and now Paul Ryan, proved itself insufficient to fix the problem either. It is time that the United States joins the rest of the first world with regard to healthcare.

The insurance companies are on-the-whole; usurious to charge vastly more than is actually necessitated by the increase in their operating expense. Insurers must all have at least some idea of what will happen to their overall expenses upon the time when they are forced to cover all of the people to whom they had previously denied coverage previously (for very well-studied reasons, indeed)! They’ve denied people coverage because they knew what the costs would be.

At this rate (no pun intended) we could very easily see a re-run of what happened with Pell Grant: educators simply ended up raising tuition at a rate commensurate with that payable by the average pupil, and thus direct health-care providers could do the same …but that’s another story. Also slightly troublesome is the fact that it is actually illegal in the US for healthcare providers to do some extremely simple market-research. It is illegal for e.g. an allergist or a dermatologist to even ask what any given competitor(s) charge for equivalent procedures.

And as for the actual costs, here is something I found quite easily off the internet:

A remaining question is whether other aspects of the ACA might also have contributed to the premium increase. Kaiser argues, plausibly, that the two factors it considered were the most direct link between the ACA and 2011 premiums. But perhaps there were indirect links as well?

I expect we will hear critics of the ACA make exactly that argument in the days ahead. Somewhat surprisingly, though, the first example I found came from the Administration. Writing on the White House blog, health adviser and deputy chief of staff Nancy-Ann DeParle pins some of the blame for higher premiums on insurance companies overestimating what their costs would be:

[list][2011 health insurance] premiums were generally set in 2010, when insurance companies thought medical costs would be significantly higher than they turned out to be. The Bureau of Labor Statistics found that the health insurance employer cost index (a measure of the price of health care services) was the lowest it has been in over 10 years in the first half of 2011. Additionally, some insurers assumed that the Affordable Care Act would dramatically raise their costs. In the end, both assumptions were wrong, but insurance companies still charged high premiums and earned impressive profits. Wall Street analysts’ review of results from the first quarter of 2011 found that 13 of the top 14 health insurers exceeded their earnings expectations, with profits that were over 45 percent higher than estimated. (emphasis added)

DeParle thus believes that the ACA did lead to higher premiums in 2011 beyond what can be explained by direct cost increases, but only because insurers overreacted. In other words, the ACA did cause premium increases beyond what can be explained by costs (since insurers would not have made the mistake about ACA costs otherwise), but the ACA doesn’t deserve the blame for those premium increases.[/list]

Source: Health Insurance Premiums Skyrocket

Some would argue that the rest of the first-world (as I said above) are being held back from economic prosperity through their government-run services…such as healthcare.

Not so.

Per capita healthcare-spending:

Look at the outlier in the above graph, Norway. A country that spends more on universal-healthcare than any other country that has it and still almost a third less (per recipient) than the US. There are obviously a plethora of reasons why nations that do indeed have universal healthcare may fare better or worse than others, but think about it logically: all of them, are spending half as much per-person than the United States is, on GDP and healthcare! Not to mention that judging by these countries’ average life-expectancies , they’re receiving somewhat improved treatment to that of the US in several important respects, and as such; I’m sure that they (countries with universal healthcare) are all VASTLY more productive, as well. (If you look at the list linked here, notice that the three countries ahead of the United States all have a more productive healthcare-system. Whether these are correlated is not clear, but I would think so). In summary, universal healthcare while expensive is clearly not nearly as expensive as its absence, and the US is an archetypal example of what happens in its absence….


The above map shows, in green, countries that administer some sort of universal health care plan. Most are through compulsory but government-subsidized public insurance plans, such as the UK’s National Health Service. Some countries that have socialized and ostensibly universal health care systems but do not actually apply them universally, for example in poverty- and corruption-rife states in Africa or Latin America, are not counted.

What’s astonishing is how cleanly the green and grey separate the developed nations from the developing, almost categorically. Nearly the entire developed world is colored, from Europe to the Asian powerhouses to South America’s southern cone to the Anglophone states of Australia, New Zealand, and Canada. The only developed outliers are a few still-troubled Balkan states, the Soviet-style autocracy of Belarus, and the U.S. of A., the richest nation in the world.


Some weeks ago, I watched Paul Ryan’s Vice-President Acceptance Speech (VPAC); and it seems to offer some horrifying prospects indeed, for America. The mere thought of this man being a mere heartbeat away from occupying the Oval Office (Romney too); is quite scary indeed. A line from William Shakespeare’s Richard III keeps echoing in my brain “Woe to the land that’s govern’d by a child!” I am tired of his cliched and grossly rhetorical approach, and as far as I could see, he laid out no discernible outline plan detailing his “solutions”. And after watching Romney’s acceptance-speech sometime afterwards, I cannot help but speculate that the “Grand Old Party” would be significantly better equipped with Condi as their candidate. Innumerable vapid banalities on “the ‘promise’ of America”, and so much outworn, tedious elocution about what it means “to be an American”.

I found this segment in particular to behighly disturbing:


      “And I will guarantee America’s first liberty, the freedom of religion.”




      “President Obama promised to begin to slow the rise of the oceans. And to heal the planet.”




      “My promise is to help you and your family.”



So…legislated Christianity (as I highly doubt that either Romney or Ryan intend to protect the Wall of Separation, or indeed the establishment clause), and uncritical denial of anthropogenic-climate-change….

So far as I can tell, that’s just about it. And the events observed since then on this topic, have been less than appealing as well. I’m struggling to see anything other than destruction to come out of these events, if these people are elected to public office (as President and Vice-President)… if there are any point that need clarification, or for example, their chances of being elected (may be discussed); please do so…

Thanks for reading.

The Dawkins/PZ Protest, 9/6/11

Fri Jun 10, 2011 4:54 pm by Th1sWasATriumph

Been a while, ain’t it?

AndromedasWake and I attended a conversation between Richard Dawkins and PZ Myers yesterday. Well, we tried. But we were slightly obstructed by the protesters who forcibly entered the theatre and then hippied up the whole damn shooting match.

Protesters? Oh, yes. You may count upon it.


Religion and support for torture

Tue Jun 07, 2011 11:01 am by Aught3

An interesting paper in the Personality and Social Psychology Bulletin details the conflicting influences of religion on support for torture. The researchers tested several possible relationships between these two factors including the influence of other variables such as education level and political conservatism. I found the results fairly surprising, let me know what you think.

The data collected was from two surveys taken in 2004 and 2008 asking 983 and 1,893 people respectively. The first effect looked at was the direct relationship between religion and support for torure. The researchers found a negative correlation on this point. That is, a religious person was less likely – on average – to support torture. This was described as an organic influence, something about the precepts of religion and opposition to torture were simultaneously appealing to the survey respondents.

However, the authors had also expected a discursive influence of religion and torture because of the popular view that religion and conservative politics ‘go together’ in the US and conservative politics lead to support for torture. When they separated out the progressive and conservative respondents, the moderating impact of religion was overwhelmed and a strong positive relationship between religion and support for torture was observed. A discursive relationship is one that arises through common perception, such as an ideological framework. Compare this to an organic relationship caused by innate features which people may not be consciously aware of. To show the three part relationship between religiosity, conservatism, and torture the researchers looked at one final factor: education level.

The authors of this study reasoned that conservatives with higher education levels would hold more consistent political views. Those with less education would be more likely to follow the common, organic, threads even if they were inconsistent with their stated political position. The data were consistent with this hypothesis showing conservative religious people who were highly educated were even more likely to support torture. So there we are, being religious is negatively correlated with supporting torture but being educated and politically engaged is positively correlated with it, at least if you are a conservative.


Malka and Soto (2011) The Conflicting Influences of Religiosity on Attitude Toward Torture. Personality and Social Psychology Bulletin.

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