Tag Archives: Inferno

Politics

Politics – Part 2: Centre right

21 Comments

Having talked about far-right parties in my first post, I wish to move slightly further toward the centre.

Centre-right parties are usually conservative parties, the examples being the Conservative Party (UK) and the Republican Party (US). I will take the specific example of the Austrian Peoples Party (ÖVP) and look at their program. Note that I can’t go through it all, it’s about 70 pages long.

A quick word about the colour system: In general, conservative parties will sport blue (UK) or black (Germany, Austria) colours. Socialist (left-wing) parties will usually have red colours. (UK, Germany, Austria) I only know of the US where these roles are reversed: The conservative party (Republicans) are red and the socialist party (Democrats) are blue.

 

The first point in the program of the ÖVP is:

Wir sind die christdemokratische Partei.

Basically: “We are a Christian democratic party.”

This is quite common in most any conservative party I know: State that you are a Christian party. The CDU and the Republicans alike emphasize this point.

Point three reads:

Wir sind die Partei der Ökosozialen Marktwirtschaft.

Basically: We stand for ökosocial markets.
This isn’t exactly what they’re doing though. Many centre-right parties, the ÖVP included, are straight capitalists, usually letting market regulate itself and only interfering if a crisis is imminent. This is also called “laissez-faire capitalism”.

It is generally true that centre-right parties focus on boosting the economy, while centre-left parties focus on using money to pay for social institutions.

Point four reads:

Wir sind die Österreichpartei in Europa.

Basically: “We are the Austria-party in Europe”

This might seem redundant, they are in Austria after all, but it’s actually a statement about two things:
1) European politics are quite difficult to understand, so I’ll refrain from that here. What you should know is that the European Parliament also contains a number of parties. The ÖVP is particularly concerned with representing Austrian interests.

2) Austrian interests are, in this case, national interests. This once again shows the strong nationalist tendencies of right-wing parties.

Point five reads:

Wir sind die Volkspartei

Basically: “We are the peoples party”

Again, this is not strictly true if you look at their voters. Generally, these voters are composed of wealthier people who don’t care too much about social infrastructure, that is to say free medicare, free public transport and so on. A newspaper article in the “kleine Zeitung” characterizes ÖVP-voters in the following way: Mostly voted for by farmers (huge lobby in Austria) and independent business people.

This is generally true of other centre-right parties. They mostly appeal to rich people (see GOP in the US) and independent business owners, while generally not appealing to the working-class. Note: This is prominently not true in the UK, where the working class seems to favour the conservative party.

Another point states: We want to boost the family as the core of society. (Fun fact: They misspelled the word “Kernzelle”, meaning core. It reads “Keimzelle”, meaning gamete. “Keim” also means pathogen, so I’m not sure what they’re telling us…)

This is similar to the more extreme-right parties: Focusing on the family (defined as man + woman + kids) and exclude same-sex couples. Opposition to same-sex marriage usually stems from the more right-wing parties such as the Republican Party, the ÖVP and FPÖ, the German CDU and, in most cases, the conservative party in the UK. (Note for the last one: There seems to be some movement going on.)

 

I think that’s enough attention devoted to the centre-right. Next up: The Green party, after which I will follow with the left wing parties.

Politics

Politics – Part 1: Right wing

13 Comments

I wanted to write about education, but I’m so bummed out with Uni that I’m not in the mood. With the elections in Austria coming up, I thought I’d share my thoughts on politics.

Most countries have around five parties, of which two usually dominate parliament. I’ll start with the right-wing parties. Let’s first remind ourselves where “right” and “left” came from. During the French revolution, the politicians on the right side of parliament were largely in favour of monarchy and the “Ancien Régime”. On the left side were those who favoured the working class.

The big clash between left and right emerged during the first and second World Wars. Russia had fallen to communist Bolsheviks and after the first World War more nationalist thought began to emerge in Germany and Austria. These ideologies were directly opposed: One was based on hierarchy and structure, the other on working together. One favoured an approach that would guarantee equity to all, the other one was proud of its achievements, even if those were only done by a select few.

Now those attitudes have hardly changed. I’ll single out the “Freedom Party of Austria” (FPÖ), look at their program and make some rather sweeping generalizations about other right-wing parties in Europe. One thing that must be pointed out right at the beginning is the incongruence between what is written and what is done.

 

Right at the beginning of the program, you can find the following: (point 2)

Wir sind dem Schutz unserer Heimat Österreich, unserer nationalen Identität und
Eigenständigkeit sowie unserer natürlichen Lebensgrundlagen verpflichtet.

Basically: We have to uphold our national identity and protect Austria.
This is a very nationalist (Note: NOT national-socialist!) view. Generally, the more right-wing the party is the more obsessed it is with security, defence and defence-budgets.

Rather unusually for right-wing rhetoric, the FPÖ then lists the minority groups in Austria and states that they’re an enrichment. Notice that that’s not the way they present themselves on the outside.
Rather more characteristic for them is the following:

“Austria is no country for immigration.” Therefore family.

What the FPÖ, and also other right-wing parties, have missed is the steady decline of births. Immigration is an essential part of our economy, without which we would collapse in mere decades.

A last point addressed is a strong favouring of Christianity and, even though they state otherwise in their manifesto, siding with Churches to oppose other religions.

A common red thread through almost all right-wing parties is the non-acceptance of other religions, especially Islam. If you want to find people opposing Islam, you’ll usually have some luck with the more right-wing parties instead of the left-wingers.

 

Point four reads:

Die Familie als Gemeinschaft von Mann und Frau mit gemeinsamen Kindern ist die
natürliche Keimzelle und Klammer für eine funktionierende Gesellschaft und
garantiert zusammen mit der Solidarität der Generationen unsere Zukunftsfähigkeit.

Basically: A Family consists of a man and a wife along with children.
Right-wing parties tend to be against same-sex marriage.

Point five:

Wir fördern Leistung in einer Marktwirtschaft mit sozialer Verantwortung, schützen
das Privateigentum und stehen für eine gerechte Aufteilung von Beiträgen und
Leistungen für die Allgemeinheit.

Basically: The protection of property and pushing markets.
Right-wing parties are usually fairly obsessed with the economy, protecting it, making it grow. This usually means a purely capitalistic market.

Point ten, incidentally the last one:

Ein Verbund freier Völker und selbstbestimmter Vaterländer ist Grundlage unserer
Europapolitik und unserer internationalen Kontakte.

Basically: Free countries and self-governing fatherlands are important.
Leaving aside the non-gender-conformist writing, this once again reinforces the nationalist concept. Where you come from is important.

These are the main headings, of which I’ve picked out the most characteristic ones. Each point is then elaborated on, as I’ve pointed out above.

I think that many of these examples will be true for other right-wing parties as well. The next four posts will be about centre-right parties (including the republicans), centre-left parties (including democrats), far-left parties and finally the greens. I will then either talk about upcoming parties, about politics in general or about anything you’re curious about. Heck, I might even put up some tools to make quick fact-checks of politicians.

Culture

Equity now?

Leave a comment

Whoever you are, we are not equals.

You might be a person living in a less economically developed country. In that case, we might be equally happy, but chances are I’m more educated (not intelligent, mind), healthy and have a better standard of living than you. We are not equal.

You might live in a more economically developed country, but you might be a woman. Although you are more likely to live a longer and healthier life and be more educated, I have better chances of getting a better-paid job, I am less likely of having to quit my job for the kids and I am less likely to work part-time. We are not equal.

You might be male, with the same education and chances of getting a job as I do. But you might be shorter than me, which increases my chances of me getting a better-paid job than you. You might be less fit, bald, etc. We are not equal.

But let us suppose that we are, in all the above mentioned respects, identical. We are both men, 22 years old, with an almost complete tertiary education degree. We are both 187cm tall, reasonably fit and with full hair. We are still not equal.

At this point, you might either understand what I’m getting at or you might be in utter despair. How are you not equal?

Well, you might be better at Basketball, while I’m better at the Trumpet. I might be better at cycling, you’re better at running. I might be a better kisser, you might be better in the sack. (Purely for the sake of comparison, of course! I excel at both.) You might be better in law, I’m better in educational studies. We are NOT equal.

We are, however, of equal value. It’s harder to make this distinction in English than it is in, for example, German. In German, we use the word “Gleich” to describe “equal”, “Gleichberechtigt” to say “of the same right” and “Gleichwertig” to say “of the same value”. In English, “equality” means all of these. I will get to one last thing it means in a second.

Everybody has a different set of talents. Whether you are a woman, chinese, a man, black, short, bald, hispanic, or anything else… there are some things you are good at and some things you are less good at. These things make you you, perhaps unique, but they do not make us equal.

Now, I talked of equality one paragraph up and mentioned a further word. Equality can also be understood as “sameness”. That’s the real danger with “equal” and “equality” I see. We miss the larger point: We are individuals and we need to be treated accordingly.

 

Joss Whedon’s speech “Equality now” is a beautiful speech about the equality of women. He explains why he writes “such strong female characters” and why he thinks we should have equality now rather than later.

However, equality doesn’t cut it.

So I suggest the much underused “equity” and I will even suggest that equality, at least in the way described above, is not what we want in many cases.

We want equality in racial matters, when it comes to LGBT-rights and so on. But ideally, we want equity when it comes to economic matters, to matters of handicaps (in whichever way they might come) and also in schooling. (Giving resources especially to kids who don’t meet the minimum requirements.) Equality can be applied wherever there is no inherent (dis)advantage on one side, while equity applies in exactly those cases.

After all this, you might ask for my justification. “Why do you want either equality or equity?”, you might ask. “Every person is the architect of his/her fortune.”

This would be the case if ours were a Darwinian society. Luckily, in my opinion, it’s not. We take care of others because we have some sense of moral duty. We take care of them because we want to be taken care of when we’re in trouble. We also do it because we ourselves profit from equity.

There’s lots and lots I could talk about on this subject, but I want to get some discussion going. Do you think this is purely semantic? If there are changes, what will they be?

Culture, Education, Reason

Education: Some facts

13 Comments

Education has been around since before written history. In one form or another, people have taught other people about stuff they know, and sometimes even about stuff they don’t or can’t know.

Real “education for the masses” has been around for only a relatively short time, since the enlightenment. I’ll talk about the enlightenment specifically in a future post, so I won’t lose time here on the why’s and how’s. In Austria, we owe our first real school reform to Maria Theresa, Empress of Austria, in 1775. She made education compulsory for all 6 to 12 year olds, which was really revolutionary in these days. She caught a lot of flack for that.

Today in the world, we have a total literacy rate of roughly 85%. That number is slightly higher for men (88.5% in 2011) and lower for women (79.8% in 2011). I won’t talk about this here, though I will remark that this imbalance is atrocious.

Global Literacy Rates in 2011

One will note that the highest one gets in this graph is “>97%” literacy. That might strike some as odd, but remember that there are a fair number of people who can’t go to school, for one reason or another, and there is a surprisingly big number of functional illiterates. (That is to say, people can’t read and write well enough “to manage daily living and employment tasks that require reading skills beyond a basic level.”)

Functional illiterates are often thought to make up anywhere between 3% and 99% of the population. In less economically developed countries (LEDC’s), to give them their proper term, the numbers of literacy in itself is low (26.2% for Mali in 2009, see page 174) and the percentage of those 26% being functional illiterates may also be high. More economically developed countries (MEDC’s) tend to have higher literacy rates (usually calculated as 99% for the HDI), but may have huge rates of functional illiterates. Wikipedia claims nearly 50% for Italy in 2003, to name but one example.

These estimates are almost certainly too high. Official figures estimate about 200,000 to 400,000 functional illiterates (plus about 80,000 illiterates) in Austria, so anywhere between 2.5% and 5%.

How many people enrol in school? The numbers are a tad more difficult here. We would need to differentiate between different ethnic groups in the US to do this topic justice, but I don’t have time for that. The general trend is: Whites enrol more than Blacks than Hispanics. (Note: I am using the language from the National Center for Education Statistics (NCES).)

At most 40% of the population are enrolled in preschool, generally over 90% are enrolled from ages 7 to 17. Then, the numbers drop rapidly. About 30% of the population continue some kind of tertiary education, though half of these are 2-3 year courses. Only 16% of adults are still enrolled between the ages of 22 and 24 (generally the time needed for a Masters or equivalent), compared to about 25% of the population in Finland.

Another thing is worth mentioning in this post: PISA. Arguably the most important assessment of secondary education today is the PISA study. Done every three years, it sets out to test students in three areas (Reading literacy, Mathematics and Science) in a standardized manner. Among the top five countries (well, regions really) in the last few years were almost always Finland, Shanghai, Hong Kong and South Korea.

Now I don’t have data on South Korea’s system of education, nor on Hong Kong or Shanghai, but I think it’s fairly safe to expect that these countries are strongly influenced by at least one socialist trend: Long compulsory education for everybody. It’s certainly true for Finland.

If you want to learn more about various education systems in the EU, I suggest Eurypedia.

I want to end on a slightly depressing note. Research shows (unsourced, I think I read it in Hattie 2007) that between 60-80% of learning achievement can be predicted by looking at the background of children. (Note: Pasi Sahlberg claims about 2/3rds, so my figure is fairly accurate.) Are they from a rich family? Does the family care about education? Do the parents hold at least one degree?

This is a travesty in two ways: It means that, no matter what teachers and the education system of today are doing, we will almost certainly lose a large portion of the children. I hope that we will find ways to make this better.

Second, it means that economic inequality has lasting consequences on your descendants. That’s unacceptable, or should be. Society should work towards making society more equal. All working toward a common goal… wouldn’t that be nice?

In future posts, I will be talking about teaching strategies, effectiveness of teaching, the Hattie study, the politics of education and different systems of education. I want to use this post as a starting point for these later discussions.

Culture, Education, Politics, Reason, Science

The EU wants to restrict seeds!!!1!!!one!!eleven

15 Comments

No reeeealy, believe me! It’s a petition after all. Here’s one of many Austrian newspaper articles on the topic.

The EU is the ultimate force of political evil in the world, we all know that. The EU wastes trillions of Euros every year on full body scanners, requires women to hand in their old sex toys and otherwise tries to infringe on our freedoms.

I am, of course, being only slightly facetious. If you look at the number of myths about the EU made up by newspapers since the early 1990’s, you might find yourself slightly overwhelmed by the stupidity floating around. One of the more ridiculous myths suggests fishing boats must carry a minimum of 200 condoms so the sailors can practice safe sex.

In short, the amount of nonsense about the EU floating around the media is staggering. If you see a story about the EU, be slightly weary.

However, I want to get back to the seeds I mentioned at the top. There is currently a lot of fear, at least in Austria, about the EU interfering with biodiversity and farmers’ rights to own/use/sell particular types of seeds.

The tabloid “Heute” “reported” that the EU wants to once again strip us of our God-given rights. Well, you can already see where this is going. The charges are the ones mentioned in the petition above: Basically, various rare seeds are to be restricted. That means no more green tomatoes and red cucumbers, etc. etc.

There’s only one problem with these allegations: They’re simply not true.

The EU law was only concerned with the compulsory registration of these seeds and the creation of norms guarding the safety and quality of them. The old, rare seeds would still be available to collectors and small enterprises, just like in the already existing laws. In short, nothing would change except that you would have to report which seeds you were planting and buying.

This was recently reported in “Der Standard”, quoting Mr. Borg: “Die Kommission schlage lediglich eine Vereinfachung der Meldepflicht vor. Ausgenommen von den EU-Vorschriften ist der Einsatz von Saatgut für private Zwecke.”

And in English: “The Commission merely suggests a simpler way of notification requirement. These prescriptions do not apply to the use of seeds for private use.”

The prescription (not a law!) has since been amended, though neither drastically nor have any of the points changed in their essence. And yet, this is counted as an “Austrian victory against the EU”. (Minister of Agriculture, Niki Berlakovic)

When will people stop talking crap and just take the time to research what is actually said?

This leads me to another point. The other day, I was talking to my uncle. He said something along the lines of “We need to know WHY laws are being passed. But companies will continue to prohibit that knowledge because that would interfere with their profit margin.”

I call bullshit on that, but that’s not my main point. I disagree with the “why?”. We do not need to know why a law is passed, at least not as a first step. Far more important is the knowledge WHAT is suggested and HOW that affects us. Knowing the exact details is often far too complicated and really up to experts, but we should be able to understand the broad gist of the laws and prescriptions, not only of the EU but most importantly in our own country. Currently, we are light-years away from that goal.

In two future posts, I will suggest ways to achieve that goal.

News, Science

The ENCODE delusion

12 Comments

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.

Pseudogenes

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:

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.

References

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.

Bostock, C. 1971. Repetitious DNA. Advances in Cell Biology 2: 153-223.

Bowler, P.J. 1975. The changing meaning of “evolution”. Journal of the History of Ideas 36: 95-114.

Bremmerman, H.J. 1987. The adaptive significance of sexuality. In The Evolution of Sex and its Consequences (ed. S.C. Stearns), pp. 135-161. Birkhauser Verlag, Basel.

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

Britten, R.J. and E.H. Davidson. 1969. Gene regulation for higher cells: a theory. Science 165: 349-357.

Britten, R.J. and E.H. Davidson. 1971. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Quarterly Review of Biology 46: 111-138.

Castillo-Davis, C.I. 2005. The evolution of noncoding DNA: how much junk, how much func? Trends in Genetics 21: 533-536.

Comeron, J.M. 2001. What controls the length of noncoding DNA? Current Opinion in Genetics & Development 11: 652-659.

Comings, D.E. 1972. The structure and function of chromatin. Advances in Human Genetics 3: 237-431.

Dawkins, R. 1999. The “information challenge”: how evolution increases information in the genome. Skeptic 7: 64-69.

Doolittle, W.F. and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.

Doolittle, W.F. 1982. Selfish DNA after fourteen months. In Genome Evolution (eds. G.A. Dover and R.B. Flavell), pp. 3-28. Academic Press, New York.

Gall, J.G. 1981. Chromosome structure and the C-value paradox. Journal of Cell Biology 91: 3s-14s.

Georgiev, G.P. 1969. On the structural organization of operon and the regulation of RNA synthesis in animal cells. Journal of Theoretical Biology 25: 473-490.

Gibbs, W.W. 2003. The unseen genome: gems among the junk. Scientific American 289(5): 46-53.

Gibson, L.J. 1994. Pseudogenes and origins. Origins 21: 91-108.

Gilbert, W. 1978. Why genes in pieces? Nature 271: 501.

Gould, S.J. 1996. Full House. Harmony Books, New York.

Gould, S.J. 2002. The Structure of Evolutionary Theory. Harvard University Press, Cambridge, MA.

Halligan, D.L. and P.D. Keightley. 2006. Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Research 16: 875-884.

Hinegardner, R. 1976. Evolution of genome size. In Molecular Evolution (ed. F.J. Ayala), pp. 179-199. Sinauer Associates, Inc., Sunderland.

Hutchinson, J., R.K.J. Narayan, and H. Rees. 1980. Constraints upon the composition of supplementary DNA. Chromosoma 78: 137-145.

Jacq, C., J.R. Miller, and G.G. Brownlee. 1977. A pseudogene structure in 5S DNA of Xenopus laevis. Cell 12: 109-120.

Jain, H.K. 1980. Incidental DNA. Nature 288: 647-648.

Jerlstrà¶m, P. 2000. Pseudogenes: are they non-functional? Creation Ex Nihilo Technical Journal 14: 15.

Kidwell, M.G. and D.R. Lisch. 2001. Transposable elements, parasitic DNA, and genome evolution. Evolution 55: 1-24.

Kondrashov, F.A. and E.V. Koonin. 2003. Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics 19: 115-119.

Kondrashov, A.S. 2005. Fruitfly genome is not junk. Nature 437: 1106.

Lefevre, G. 1971. Salivary chromosome bands and the frequency of crossing over in Drosophila melanogaster. Genetics 67: 497-513.

Loomis, W.F. 1973. Vestigial DNA? Developmental Biology 30: F3-F4.

Makalowski, W. 2003. Not junk after all. Science 300: 1246-1247.

Max, E.E. 2002. Plagiarized errors and molecular genetics: another argument in the evolution-creation controversy. Talk.Origins Archive.

Moore, M.J. 1996. When the junk isn’t junk. Nature 379: 402-403.

Nowak, R. 1994. Mining treasures from ‘junk DNA’. Science 263: 608-610.

Ohno, S. 1970a. Evolution by Gene Duplication. Springer-Verlag, New York.

Ohno, S. 1970b. The enormous diversity in genome sizes of fish as a reflection of nature’s extensive experiments with gene duplication. Transactions of the American Fisheries Society 1970: 120-130.

Ohno, S. 1972. So much “junk” DNA in our genome. In Evolution of Genetic Systems (ed. H.H. Smith), pp. 366-370. Gordon and Breach, New York.

Ohno, S. 1973. Evolutional reason for having so much junk DNA. In Modern Aspects of Cytogenetics: Constitutive Heterochromatin in Man (ed. R.A. Pfeiffer), pp. 169-173. F.K. Schattauer Verlag, Stuttgart, Germany.

Ohno, S. 1974. Chordata 1: protochordata, cyclostomata, and pisces. In Animal Cytogenetics, Vol. 4 (ed. B. John), pp. 1-92. Gebrà¼der Borntraeger, Berlin.

Ohno, S. 1982. The common ancestry of genes and spacers in the euchromatic region: omnis ordinis hereditarium a ordinis priscum minutum. Cytogenetics and Cell Genetics 34: 102-111.

Ohno, S. 1985. Dispensable genes. Trends in Genetics 1: 160-164.

Patrushev, L.I. and I.G. Minkevich. 2006. Eukaryotic noncoding DNA sequences provide genes with an additional protection against chemical mutagens. Russian Journal of Bioorganic Chemistry 32: 1068-1620.

Petsko, G.A. 2003. Funky, not junky. Genome Biology 4: 104.

Raup, D.M. 1991. Exctinction. W.W. Norton & Co., New York.

Roels, H. 1966. “Metabolic” DNA: a cytochemical study. International Review of Cytology 19: 1-34.

Ruse, M. 1996. Monad to Man. Harvard University Press, Cambridge, MA.

Shapiro, J.A. and R. von Sternberg. 2005. Why repetitive DNA is essential to genome function. Biological Reviews 80: 227-250.

Sharma, A.K. 1985. Chromosome architecture and additional elements. In Advances in Chromosome and Cell Genetics (eds. A.K. Sharma and A. Sharma), pp. 285-293. Oxford and IBH Publishing Co., New Delhi.

Slack, F.J. 2006. Regulatory RNAs and the demise of ‘junk’ DNA. Genome Biology 7: 328.

van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most “Dark Matter” Transcripts Are Associated With Known Genes. PLoS Biology 8(5):1-21.

Vinogradov, A.E. 1998. Buffering: a possible passive-homeostasis role for redundant DNA. Journal of Theoretical Biology 193: 197-199.

Walker, P.M.B., W.G. Flamm, and A. McLaren. 1969. Highly repetitive DNA in rodents. In Handbook of Molecular Cytology (ed. A. Lima-de-Faria), pp. 52-66. North-Holland Publishing Co., Amsterdam.

Walkup, L.K. 2000. Junk DNA: evolutionary discards or God’s tools? Creation Ex Nihilo Technical Journal 14: 18-30.

Wickelgren, I. 2003. Spinning junk into gold. Science 300: 1646-1649.

Wieland, C. 1994. Junk moves up in the world. Creation Ex Nihilo Technical Journal 8: 125.

Williams DL, Slayden RA, Amin A, et al. 2009. “Implications of high level pseudogene transcription in Mycobacterium leprae”. BMC Genomics 10: 397.

Woodmorappe, J. 2000. Are pseudogenes ‘shared mistakes’ between primate genomes? Creation Ex Nihilo Technical Journal 14: 55-71.

Woolfe, A., M. Goodson, D.K. Goode, P. Snell, G.K. McEwen, T. Vavouri, S.F. Smith, P. North, H. Callaway, K. Kelly, K. Walter, I. Abnizova, W. Gilks, Y.J.K. Edwards, J.E. Cooke, and G. Elgar. 2005. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biology 3: e7.

Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Régnault B, Devaux F, Namane A, Séraphin B, Libri D, Jacquier A. 2005. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121: 725-37

Yunis, J.J. and W.G. Yasmineh. 1971. Heterochromatin, satellite DNA, and cell function. Science174: 1200-1209.

Zuckerkandl, E. 1976. Gene control in eukaryotes and the C-value paradox: “Excess” DNA as an impediment to transcription of coding sequences. Journal of Molecular Evolution 9: 73-104.

Zuckerkandl, E. and W. Hennig. 1995. Tracking heterochromatin. Chromosoma 104: 75-83.

Zuckerkandl, E. 1997. Junk DNA and sectorial gene expression. Gene 205: 323-343.

 

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.

Medicine, Science

The great vaccination scare

Leave a comment

Most of you will have heard of the MMR vaccine controversy. A man, Dr. Wakefield, suggested that the MMR vaccination increased the likelihood of autism in infants and children. People stopped vaccinating their kids, which resulted in a few thousand cases and a few deaths. All of them could have been avoided, had it not been for Dr. Wakefield.

As we know, people don’t learn from their mistakes, the deep-rooted fear still possesses them. In a previous blog entry, I talked about my homeopath/M.D. aunt, among other things. She’s a lot of things I could make fun of, but one of the things that makes me sad is that she also opposes vaccines. She went to Kenya without a single vaccination, even though yellow fever is a deadly disease. Her whole family is the same, they all oppose vaccinations.
Recently, I talked to a friend of mine. She’s also against vaccinations, because they can “harm your immune system”.

Let’s look at anti-vaccers claims:

Vaccines are not effective, vaccines are not safe, vaccines are not moral or vaccines are against my religion.

We can dismiss the last two claims out of hand. If you don’t want to use them due to your religion then your religion is pretty fucked up.
I also reject the case for personal liberty. If your idiocy is putting other people at risk, you have no say. Period. Your rights should be stripped away to protect the rest of the population.

So we’re left with two questions:

1) Are vaccines effective?

2) Are vaccines safe?

The efficacy-question is easily answered: Vaccines are among the few things to come out of the pharma-industry that are so very obviously effective that we shouldn’t even have to think about this.

Forbes recently posted a short article on the topic. The following info-graphic was compiled from a recent article, linked in the Forbes-post.

Vaccines Info-graphic

Smallpox was once one of the most prolific killers, with an estimated 300-500 million killed just from Smallpox alone. And now, it’s virtually eradicated.

Thanks to vaccines? I think the above is ample evidence to that extent, but there’s more. The following graphic (Wikipedia) was compiled for the prevalence of rubella, but it could equally have been compiled for any other vaccine. It always follows the same path: A vaccine is introduced and given, the prevalence of the disease goes down.

Prevalence of rubella

 

So on to the second argument: Safety.

When I was a baby, I was immunized against MMR. The batch I received was tainted, I fell ill. I could have died, but was given medication and survived. But even in the best of circumstances, people can have adverse reactions to the immunizations.

Here’s the deal though: These reactions are incredibly unlikely to happen.
A paper from a  few years ago discussed this and came up with the following conclusion: “[T]he expressed doubts about the safety of vaccines are unjustified.”
That’s it really. Vaccines are an effective and safe way to counter several potentially deadly diseases. To eradicate these diseases, we all need to take the vaccines. If you don’t immunize yourself, you not only put yourself at risk but also the rest of the population, by allowing the disease to survive.

I don’t think any argument can be made that vaccinations are dangerous or ineffective. If you think there is, please, I need a laugh right about now.

Culture, History, News, Politics, Religion

Habemus Papam! And what do believers say?

19 Comments

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.

Culture, Education, Politics, Random

Have some vision!

15 Comments

As I might have said already, I’m training to become a teacher. In my studies, I’m often confronted with interesting kids (both negative and positive) and equally interesting colleagues (also both negative and positive).

The funny part? With kids, the positive outweigh the negative about 10:1 or 20:1. But teachers? It’s the other way around, 1:10 or 1:20. The amount of stupid, unmotivated, socially incompetent, bored and vision-less teachers I’ve met is appalling. I recounted the one event where a teacher declared us to be “different from other animals because we evolved”. That’s fairly stupid, but it can easily be corrected by a somewhat competent biology teacher.

But what happens if you get teachers who are unwilling to teach a certain concept simply because it’s “hard to teach”? No kidding, that’s what a teacher said on Thursday, March 7th. Note that this took place one day before International Woman’s Day. Here’s the conversation from a seminar. The teacher (~30 years of experience) was in the audience:

Teacher: So basically, I don’t teach students from other countries that it’s important to treat women in the same way as men because their parents will come to school and complain. Plus, the parents don’t even want to shake hands with me because I’m a woman so why should I bother?

* Nods of approval from the audience*

Me: I don’t want to sound offensive, but what you’re doing is actually against the law. The Austrian curriculum says, among other things, very specifically that we have to teach “tolerance towards others, minorities and other cultures”. I’d suggest that “others” includes women. A different law (which I’m unable to recall at this moment) also states that we have to raise kids to be “mündige Bürger”, which I’d translate as mature/responsible citizens. Part of that is adhering to the basic norms we’ve got in our culture, in this case treating women equally well as men.

The teacher wasn’t able to respond, obviously, so that was that.

Now I put it to you that this is not exclusive to teaching. You’ll have idiots in every job, people who’ll stall progress. But I’d also argue that teaching is so incredibly important that we have to single it out. We raise the next generation, we are responsible for the future. If we fuck up badly, everything is potentially fucked.

End rant.
My message? Have some vision! Don’t let other people wear you down, don’t forget the ideals you had when you were young. Stick to them, no matter how hard it is.

Education, Medicine

Evidence-based medicine: Introduction Part 2

14 Comments

In my first post on medicine I talked about the various dangers that can arise from medicine that’s neither effective nor particularly harmful. In my second post, I talked about one particular alternative medicine, PSE, showed that it’s not based on any evidence whatsoever and most likely does not work, though that can’t be confirmed because in it’s 15-year runtime it has yet to be properly and fairly tested. That’s fairly common in alternative medicine.

In this post, I want to tackle an argument you can often hear from advocates of alternative medicine: “Why should I want evidence when all the “evidence-based” medicine isn’t based on any actual evidence?” I’ll also give an introduction into evidence-based medicine, albeit a very brief one.

For the purpose of this post, I’ll recommend two excellent books:

Goldacre, B. (2012) Bad Pharma – How drug companies mislead doctors and harm patients

Evans, I., Thornton, H., Chalmers, I. & Glasziou, P. (2006) Testing Treatments – Better research for better healthcare

About 90% of my examples come from these two books, mainly because they give nearly all the relevant sources. (Meta studies and so on)

As Evans et al. document: (P.13-14) As a parent, the most horrible thing that can happen to you is your child dying. Naturally, parents will immediately do what a doctor tells them if it’s said to reduce infant suffering and death. In 1946, Dr. Benjamin Spock‘s book “Baby and child care” suggested babies sleep on their backs. In 1956, he revised that statement, saying:

There are two disadvantages to a baby’s sleeping on his back. If he vomits he’s more likely to choke on the vomitus. Also he tends to keep his head turned towards the same side… this may flatten the side of the head… I think it is preferable to accustom a baby to sleeping on his stomach from the start.

That sounds like incredibly sound advice, which is why many parents (millions?) opted to do so. However, there was one serious flaw: This practice, never evaluated, led to an estimated 50,000 deaths. A first study suggesting harm was published mid 1960’s, a second in the early seventies, two further ones in the mid 80’s. It was only properly acted on in the mid 90’s. (In some cases until 2002!)

Now one might argue that this is a case of “evidence-based medicine” gone wrong. I disagree, it’s precisely the opposite. Here, no evidence or very shoddy evidence was provided, which eventually led to tens of thousands of deaths. Had the evidence been appraised correctly right away, many if not most of these deaths might have been avoided.

There are dozens of examples like this in the two books, so I won’t go through them. The authors have gone to great pains to document these cases and I recommend you read about them yourselves. I just want to bring this back to the point I was trying to make: Evidence-based medicine can only function if we look at the evidence carefully and without bias, and if we then act on the evidence as swiftly as possible.

This system is by no means perfect, because humans will always find a way to either intentionally interfere with the process (for political or monetary reasons) or to be so stupid as to fuck up. However, it’s better to have a system that’s based on evidence we can theoretically gather (evidence-based medicine) than basing it on a system that involves nothing more than guesswork. (alternative medicine)

At this point, I should probably point out how incredibly fragile this review process is. Ben Goldacre documents: (P. 69)

Imagine you’re conducting a study on a particular drug. Let’s call it pregabalin, a drug to help diabetics handle pain when their nerves have been affected by the disease. You gather test subjects, you double-blind the study, you do everything you’re supposed to. But some subjects drop out of the study, due to various reasons. It might be that they still feel pain and don’t want to continue or the side effects might be too severe. Whatever the reason, you’re now faced with a problem. You’ve got half a dataset for the drop-out patient. How can you incorporate the results in the study?

The researcher, let’s call him Pfizer, does a clever thing: He uses the “last observation carried forward”-method. That’s a fancy sounding name for “I’ll put down the last result I got into every column. Basically, the patient had pain levels of 10, 9, 8, 7, 6, 5, 5, 6, 5, and then dropped out. So Pfizer fills in the last six data-points with all 5’s. Before the study, you will notice, the patient had pain levels of 10.

The research then gets published and your drug looks quite good indeed. But wait! what’s that? Some researchers disagree with your method? But why? Well, the reasoning is this: The patient dropped out, so their pain level is back to 10. Obviously, the side effects were worse than the pain and they stopped using the drug. So we have to put all 10’s for the last six data-points instead of all 5’s. That’s called the “baseline observation carried forward”-method.

The difference between the two methods is staggering: With the LOCF the drug gets overestimated by nearly 25%!

That, you will agree, is quite a lot. Once again it shows: Medicine must be based on the best possible evidence, not on guesswork and shoddy methods.

I’ll leave you with a few points:

  • Biased testing will leave you with incorrect data, thus putting patients at risk.
  • All medicine should be tested and carefully evaluated. Failing to do so puts patients at risk and should be persecuted.
  • Trusting doctors blindly is not always a good choice. Ideally, your doctor should be able to show you what research (s)he’s basing his/her decision on.
  • Basing therapies on theories instead of real-world outcomes is again putting patients at risk.
  • As suggested in my first post, using treatments that are neither directly harmful nor beneficial is also not recommended.
  • Established treatments are not necessarily beneficial: Check and re-check. I explained that partially in my second post.
  • Tests should be as fair as possible, that is to say: Randomised (double-blinded) Controlled Tests (RCT’s), comparing like with like, meta-studies, etc. This requires that potential researchers and future doctors be trained in the best available methods.

I’ll leave it at that and once again recommend the two above mentioned books. Remember, all science needs evidence and we need laws to ensure the best standards.  We need institutions like the Cochrane Collaboration to appraise the available evidence without interference from commercially or politically driven institutions. Read “Bad Pharma”, it’ll really shock you.