#PLOSGenetics: The Case for Junk DNA

This is the paper to read: Palazzo & Gregory’s The Case for Junk DNA. It clearly and logically lays out the complete argument from evidence and theory for the thesis that most of the genome is junk. It’s not revolutionary or radical, though: the whole story is based on very fundamental population genetics and molecular biology, and many decades of accumulated observations. And once you know a little bit of those disciplines — you don’t need to be a genius with a great depth of understanding — the conclusion is both obvious and in some ways, rather trivial.

Here’s that conclusion:

For decades, there has been considerable interest in determining what role, if any, the majority of the DNA in eukaryotic genomes plays in organismal development and physiology. The ENCODE data are only the most recent contribution to a long-standing research program that has sought to address this issue. However, evidence casting doubt that most of the human genome possesses a functional role has existed for some time. This is not to say that none of the nonprotein-coding majority of the genome is functional—examples of functional noncoding sequences have been known for more than half a century, and even the earliest proponents of “junk DNA” and “selfish DNA” predicted that further examples would be found. Nevertheless, they also pointed out that evolutionary considerations, information regarding genome size diversity, and knowledge about the origins and features of genomic components do not support the notion that all of the DNA must have a function by virtue of its mere existence. Nothing in the recent research or commentary on the subject has challenged these observations.

The whole ENCODE debacle, in which hundreds of millions of dollars was sunk into an effort to identify the function of every bit of the genome, was a PR disaster. Larry Moran asks how Nature magazine dealt with the errors; the answer seems to be with denial. Authors of the ENCODE report are claiming they were “misunderstood & misreported” and that they aren’t “backing away from anything”.

I’m not too dismayed that science journalists didn’t understand how the claims of ENCODE conflicted with evolutionary biology, since I don’t expect journalists to have the same focus on the science (this is not a knock on science journalism; I have a lot of respect for the good practitioners of the art, but just that they have different priorities than the working scientists who have to deal with the background details). But what really shocks me is that big-name genomics researchers, people who get awarded lots of money to study the structure of the genome, don’t understand the fundamentals laid out for them in the Palazzo & Gregory paper. It’s not that I expect every scientist to know the entirety of a gigantic field — heck, I get confused and lost every time I read a bioinformatics paper — but these are scientists paid in big money and prestige to study genome function who don’t have a grasp on the evolutionary constraints on genome function, which seems to be a rather critical omission. And these scientists without a clue get elected to the Fellowship of the Royal Society.

How does that happen? I had this fantasy that science was a meritocracy and that great scientists advanced by having deep knowledge and doing great work, but it seems another way to succeed is leap into a new field and bamboozle everyone with technology.

I am so disillusioned.

Idaho, too?

Good news from Idaho.

U.S. Magistrate Judge Candy Dale has ruled Idaho’s ban on gay marriage is unconstitutional.

In her 57-page decision, Dale stated, "Idaho’s Marriage Laws withhold from them a profound and personal choice, one that most can take for granted. By doing so, Idaho’s Marriage Laws deny same-sex couples the economic, practical, emotional, and spiritual benefits of marriage, relegating each couple to a stigmatized, second-class status. Plaintiffs suffer these injuries not because they are unqualified to marry, start a family, or grow old together, but because of who they are and whom they love."

Especially delicious: Bryan Fischer is an Idaho wackaloon, and his radio meltdown will be spectacular, I’m sure. He’s already taking it personally on Twitter.

What blessed drivel is this?

haploidchrist

Every once in a while, an obscure science journal somewhere just has to demolish their reputation by allowing their editors to publish garbage. Case in point: The Journal of Maternal-Fetal & Neonatal Medicine, the official journal of the European Association of Perinatal Medicine, has published an editorial titled, “Can modern biology interpret the mystery of the birth of Christ?” It’s five pages of embarrassingly goofy nonsense. Nonsense from the very first paragraph:

With the advent of Enlightenment, the intellectual movement that challenged principles and views grounded in tradition and faith and affirmed that knowledge should be advanced through a scientific method, science and religion began to drift apart and today, they are often considered irreconcilable. We believe that, since both aim at finding the same truth, whether by evaluating natural processes or through revelation, a positive dialogue can and should be established.

And this article is apparently intended to demonstrate that they aren’t just considered irreconcilable, but are irreconcilable. That last sentence is just plain wrong. Science attempts to determine verifiable truths that can be objectively and independently examined and tested. Religion claims to have the truth already, in their musty dusty old books, and attempts to manipulate the evidence to make it fit their preconceptions. Their goals are contradictory, and since religion will always attempt to corrupt the evidence to reconcile it to their dogma, we should not establish a dialog at all — we should simply dismiss this theological bullshit.

For example, this article assumes that there existed a person named Jesus who was born of a virgin and a god; despite the fact that its conclusion is that nothing in biology can explain this phenomenal claim, it doesn’t reject the hypothesis. It can’t; it’s taken as a given. It blithely cites the Bible as reasonable evidence throughout (Hint: any science article that includes the Holy Bible (4 times!), the Catholic Catechism, the Catholic Encyclopedia, and CARM.org in its reference list, alongside articles from Cell and Nature, ought not to be trusted), and takes for granted the most ridiculous articles of the Christian faith.

There is some entertainment value, though. The review of the literature attempting to explain the Virgin Birth is amusing.

Aiming high within the field of reproductive biology, we decided to attempt a scientific analysis of the first, most miraculous and fundamental of all events described in the New Testament, that defined by John at the beginning of his Gospel: “And the Word became flesh”. We are definitely not the first to address this complex topic. For instance, Edward Kessel and Robert Berry have amply discussed fundamental aspects of the Incarnation and mentioned several mechanisms by which the virgin birth of a male child might have occurred. Kessel, in particular, held the opinion that “Jesus was not only conceived as a female but remained chromosomally such throughout life. Through the natural process of sex reversal Jesus became male, not instead of female but as well as female, assuming the phenotype of a man while retaining the chromosomal badge of a woman. Thus Jesus was born and lived as the androgynous Christ”. Berry, on the other hand, believes that “Some form of distinctiveness like a Virgin Birth is theologically required if Jesus is to be divine as well as human, and there are several mechanisms by which the virgin birth of a male child could occur”. In his opinion, “The reason for recognising these is not to suggest that God necessarily used any of them, but simply to point out that apparent scientific difficulty should not determine the acceptability of a theological concept”.

You know, when you have to resort to increasingly twisted and complicated rationalizations to explain an undemonstrated event, wouldn’t it be easier to simply declare the event unlikely to have occurred, especially when there is absolutely no evidence for it, other than a word-of-mouth claim? At least, that’s what a scientist would do.

These authors, after going over some of the basic facts of sex determination, have another source to fall back on, though. When evidence fails, yank some hokum out of the Bible.

Even theists consider the birth of Jesus a “double miracle”, in the sense that, even if parthenogenesis could be possible in humans, the offspring of such an event would be a female, not a male. In this respect, there is a somewhat obscure prophecy by Jeremiah, a Jewish prophet almost a contemporary of Isaiah. He wrote: “The Lord has created a new thing upon the earth: a woman shall compass a man”. This text has been interpreted in many opposing ways, but one intriguing option, put forward by Ewald is “a woman shall change into a man”. Although this interpretation has been considered hardly faithful to the original text, if correct, it would be a premonition of what might have occurred in the case of Jesus, a “parthenogenically” born man.

Yeah, try telling that to the Christians. Maybe they’d quit freaking out over transgender.

Really, the whole idea makes no biological sense at all. The only way this parthenogenesis thing could work is if Mary had a copy of SRY to pass along (but then she’d be male!), but then maybe she had androgen insensitivity syndrome too (but then she’d be sterile!) but then she’d pass that on to Jesus (who would be female!) unless he had a reversion mutation. It’s a long chain of malarkey.

To their credit, the authors also recognize that none of the explanations are worth a good god damn.

The reason we attempted a scientific analysis of this mystery was simply the hope that a review of present knowledge of parthenogenic mechanisms may stimulate a debate among theologians and advance the search for truth. Limiting ourselves to biology, the only conclusion we can reach is that – after reviewing present knowledge about parthenogenesis – we are unable to identify any known natural biological mechanism that can account for the virginal birth of Christ.

Very good. So why did you waste our time publishing this tedious codswallop?

Take the next step. Reject the hypothesis.

Benagiano G, Dallapiccola B (2014) Can modern biology interpret the mystery of the birth of Christ? J Matern Fetal Neonatal Med. Apr 30. [Epub ahead of print]

The next step in our descent

We’ve already got the right wingers outright denying science. They couldn’t get any worse, could they? Have we hit bottom yet? No. They could be accepting the evidence for all the wrong reasons. Expect this to be the new normal for the far right in a few years.

Christian Post blogger Michael Bresciani writes this week that changes in the climate are indeed taking place, but not due to human activities such as fossil fuel emissions. Instead, he says extreme weather is the result of “homosexuality, abortion [and] general sexual preoccupation,” which according to Bresciani is bringing about the End Times and the coming of the Antichrist.

I hope it’s a few years. But you never know — with the midterm elections coming up, the Republicans may embrace it as a winning strategy.