“The Designer’s Detritus” – my latest Nature Education post on ENCODE, junk DNA and intelligent design

I said I’d tell you when it was published – and it’s been published! Somewhat surprisingly, I was asked by my friend Khalil to write up my thoughts on the whole ENCODE project/junk DNA/the-human-genome-is-80%-functional fiasco for the Student Voices blog, but from the perspective of what intelligent design proponents were taking from it all. If you’ve been following pro-ID blogs Evolution News and Views and Uncommon Descent lately, there’s been little end to the victorious proclamations – because, as we all know, the more functional the genome is, the more likely ID is to be true, right?

Uh, yeah. Right. Sure. This is one of the issues I discuss in my Nature Education post (and don’t forget that I’ve discussed it on Homologous Legs before too), along with some other things.

Here’s a taste to get you in the mood:

Where to start? It’s unlikely that you’ve missed any of the extensive media coverage the Encyclopedia of DNA Elements (ENCODE) project has received over the past two weeks, after the international team of scientists responsible published 30 papers in high-profile journals detailing their efforts in mapping the activity of the human genome in over 100 cell types. Nearly every newspaper, online news site and vaguely science-y blog has written something about the accomplishment, with most focusing on what has become, unarguably, ENCODE’s most controversial “finding”: that over 80% of the genome is functional.

A good proportion of the biology community hit back at the claim, with the blogs of biochemist Larry Moran and evolutionary geneticist T. Ryan Gregory providing some of the more comprehensive critiques (which are spread across multiple posts on their blogs – have a look through their archives if you’re interested in the details). The consensus amongst the critics is that the leaders of ENCODE have a very loose definition of “functional”, under which it is likely most possible DNA sequences will fall, including those uncontroversially deemed “junk DNA”, simply due to the noise and imprecision inherent in various biological processes like transcription. Somecritics have even gone so far as to propose the Random Genome Project, a null hypothesis test for the “80% functional” claim essentially based around the question “What proportion of a randomly generated genome, on average, would be assigned function based on ENCODE’s criteria?” If the answer turned out to be around the 60-80% mark, it would cast serious doubts on the claim that most of our genome is functional.

I have good reason to think that there might be a response to this piece forthcoming from ENV in the next few days – like always, I’ll keep you all posted…

Open up my spine and plug me in again

It’s now officially a holiday period for me (for some curious reason my university is giving everyone a two-week mid-semester break – but no one’s complaining), but I’m still busy as hell with multiple projects, including coursework, the YAS relaunch, the podcast and just generally trying not to go insane. So! Here are some more interesting/relevant things I’ve stumbled across in the past few days.

Standford University has a free, online writing course through Coursera called “Writing in the Sciences” starting on the 24th of September! It’s free! And online! And seems pretty cool! I’ve signed up (not sure how much time I’ll be able to devote to it, but we’ll see) and you should too, if you’re interested in improving your science writing skills – there’s always more to learn.

Speaking of science writing, Ed Yong has a great post up on his fabulous blog Not Exactly Rocket Science about “photosynthetic” aphids and the dream of photosynthetic humans. I previously touched this topic on Episode 58 of The Pseudo Scientists, but Ed goes into a bit more detail than I did. Plus, he’s a professional. Always go with the professional.

Speaking of The Pseudo Scientists, Episode 59 was released on Sunday! Belinda, Tom, I and special guest Ted Janet talk about the ENCODE project and junk DNA, nano-ink, transgenic camels and Ted’s time at The Amaz!ng Meeting 2012. If you’ve never listened to the show before, uh, make sure you do, I guess? I put a lot of work into it, so I’d be nice to have people listen. You know, if you want. It’s your time, after all. (Oh, what’s this, a handy link to the iTunes page, where you can subscribe to the podcast? Dear me.)

(Speaking of ENCODE, I have a new post for Nature Education’s Student Voices on ENCODE, junk DNA and intelligent design creationism coming out in the next couple of days – I’ll draw your attention to it when it goes up.)

Speaking of the Young Australian Skeptics, we’re having a sale for our book, the YAS’s Skeptical Blog Anthology (featuring yours truly, but also featuring Phil Plait, Evan Bernstein, Daniel Loxton, Barbara Drescher and more!), at the moment – enter the code PIRATA at checkout to receive 15% off! Offer closes September 21st, so hurry, I guess? It’s truly a great book, and sales help support both the YAS blog and the podcast, as well as our failing egos.

And because this wouldn’t be a Homologous Legs post without a reference to good ol’ St. Vincent, here’s a video from the first date on St. Vincent and David Byrne’s Love This Giant tour. You do want to see Annie Clark and David Byrne play the theramin together, don’t you? Thought so.

You can watch more of the videos from that show here! (I know, it’s Pitchfork, but what’cha gonna do?)

These Weeks in Intelligent Design – 18/05/11

Intelligent design news from the 28th of April to the 18th of May, 2011.

Finally! It’s back again, your fix of ID news and discussion. To make up for my three-week-long absence, this post will cover five of the top ID blog posts from the past three weeks. Lucky for me then that it hasn’t been an especially busy time for the ID community during my break – otherwise I’d have a much bigger job on my hands.

Anyway, enough grovelling, let’s get into it.

Today’s posts are about Osama bin Laden and junk DNA, Oxford University and evolutionary mathematics, dissent in the evolutionary ranks, enzyme evolution, and, of course, junk DNA.

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This Week in Intelligent Design – 27/04/11

Intelligent design news from the 21st of April to the 27th of April, 2011.

The Discovery Institute has been extremely relaxed with its posting over the last week – partially explaining why this is slightly late, there was no massive compulsion on my part to hastily set the record straight on certain blog posts before other new items swallowed the spotlight – and whether this is an external representation of the internal busyness of the organisation, I’m not sure. Perhaps Casey Luskin was too busy doing proper science-attorney things too blog much this week.

But it doesn’t really matter, there’s enough meat for me to sink my metaphorical blogging teeth into. Also, I remember the last time there was a slump in blogging output from the Discovery Institute: I predicted wonderful things were about to happen, but I was wrong. So, I’ll try not to read anything into it.

This week’s TWiID covers pseudogenes and “Darwinian assumptions”, enzyme evolution and ID, and the traditional religious bias of the Discovery Institute.

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This Week in Intelligent Design – 20/04/11

Intelligent design news from the 14th of April to the 20th of April, 2011.

Another week, another lot of ID blog posts to wade through. Not a lot I want to mention in this intro, particularly, except for perhaps this recent post of mine responding to an Uncommon Descent post about ID’s supposed scientific predictions. It was going to be included in this post, but it needed a larger amount of specific attention, given how important the topic is.

Other than that, this week wasn’t particularly noteworthy. Nothing that changed the ID/evolution game too much, just some ideas to consider. Robert Crowther wrote about the difference between promoting ID and teaching criticisms of evolution, Casey Luskin attacked the NCSE’s Steve Newton for over/misusing the word “creationist”, and Jonathan Wells’ new book on junk DNA got a flattering plug, possibly foreshadowing another book-promoting frenzy…

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Carnival of Evolution No. 34 out now at Quintessence of Dust

The Carnival of Evolution for April is up at Quintessence of Dust! Head on over there for junk DNA, kin selection, brains, penises and archaea.

The next Carnival of Evolution (for May) will be at Lab Rat. There isn’t a host announced yet for June though, so put your name down if you’d like to host, and submit your evolution-themed posts as soon as humanly (and humanely) possible.

This Week in Intelligent Design – 26/10/10

Intelligent design news from the 20th of October to the 26th of October, 2010.

It’s slim pickings tonight on the ID front – for some reason the Discovery Institute and friends decided to only post whimsical complaints about minor issues this week, without making any outlandish claims. Well, less outlandish claims than usual – if none were made you might not be reading a blog post right now and I certainly wouldn’t be writing one.

Because this is going to a shorter, less intense TWiID than usual, I’ll be testing out Homologous Legs’s new footnote capabilities. Hopefully they’ll be used for good and not evil.1

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  1. Or snark.

The Curious Case of the Designer’s Bad Design

You hear it a lot, the claim that bad design is evidence against intelligent design. Jerry Coyne and Richard Dawkins, two of the most well-known educators about evolutionary biology, regularly mention it in their books and other writings, and so do numerous other defenders of evolution, striking back at the apparently growing intelligent design (ID) movement that is threatening science education in the US and across the globe.

The argument from bad design is as follows. If life were designed by an intelligence, particularly a supernatural intelligence, organisms wouldn’t be observed to have redundant organs, clumsily constructed systems and life-threatening faults with the ways their bodies work. Vestigial structures, like the tiny hind leg bones of whales or the flimsy wings of flightless ratites, wouldn’t exist, and the vast portions of genomes that do nothing, such as the broken remains of ancient retroviruses, wouldn’t be there. Life looks nothing like it was designed by an intelligence.

Fortunately for intelligent design, some ID proponents have an answer to this problem, as expressed here by Robert Crowther, the Director of Communications for the Discovery Institute’s Center for Science & Culture:

All a response…this [bad design argument] really requires is to post a few photos of clearly designed items that have had amazing, spectacularly bad problems. (The Hindenberg for instance. Or any Toyota apparently.) How stupid, yes I said stupid, do you have to be to equate bad design with no design?

In other words, bad design is not a problem for intelligent design because, while many objects have problems associated with them, these problems don’t take away the fact that the objects were designed. Intelligent design is compatible with a spectrum of the Designer’s possible competence, so pointing out a biological system that has flaws does not constitute evidence that the system was not designed.

This is a powerful and intuitive argument to defend “pure ID”, a strain of ID I’ve defined previously. Pure ID does not identify any qualities or characteristics of the Designer, and as such does not, within itself, allow for the distinction between a natural designer (an extraterrestrial intelligence) or a supernatural designer (a deity). Bad design is not a problem for pure ID because the vague nature of the Designer encompasses any and all levels of competence, disassociating itself from the necessity of perfect design. It is probably because of this fact that the Discovery Institute puts forward the “pure” strain of ID:

…the scientific theory of intelligent design does not claim that modern biology can identify whether the intelligent cause detected through science is supernatural.

Unfortunately for pure ID, its refusal to identify the Designer renders it unable to make predictions about any designs it is purported to explain. Pure ID proponents, like those at the Discovery Institute, cannot produce a list of attributes that an organism would have if it were designed, besides the presence of “complex and specified information” (CSI). However, this is not a positive prediction made by ID itself, but a veiled, direct argument against evolutionary theory, which they maintain cannot explain CSI. Their reasoning continues, often hidden in the background of the argument, that as evolutionary theory and ID are the only two options for explaining the characteristics of life, the presence of CSI must support ID. This argument is neither logically valid nor sound, but this is rarely acknowledged by ID proponents.

With pure ID unable to make predictions, it wouldn’t be a stretch to assume that the Discovery Institute doesn’t try to mislead the public into thinking that it does. However, this is not the case. Casey Luskin, the Program Officer in Public Policy and Legal Affairs for the Discovery Institute and one of its most prolific bloggers, often writes about new discoveries in biology, mostly to do with “junk DNA” (DNA that does not appear to have a biological function) that he claims are predicted by intelligent design.

In “The Positive Case for Design” (PDF), Casey claims that ID predicts:

Intelligent agents typically create functional things (although we may sometimes think something is functionless, not realizing its true function) [therefore] much so-called “junk DNA” will turn out to perform valuable functions.

Ignoring for the moment the properties of pure ID, this runs contrary to the claims made by Robert Crowther, above. Either intelligent agents are required produce things that are functional, as claimed by Casey, or intelligent agents are not required to produce things that are functional, as claimed by Robert. Since neither of these ID proponents have ever critiqued each other and they write on the same blog, one must assume they are in agreement.

But how can this be so? For Casey’s ID prediction to be useful and scientific, intelligent agents (ie. the Designer) must always produce functionality. However, Robert puts forward his claim that intelligent agents do not have to produce functionality (ie. that bad design is acceptable) in order to counter the claim that bad design in biological systems is not evidence against ID. Both cannot be correct – either ID makes a prediction and is open to scientific criticism, or it does not make a prediction and is immune from scientific criticism.

Whoever is right depends on what definition of ID is being used. If pure ID, then Robert is correct and bad design is acceptable. But if it is “ID creationism”, a strain of ID that claims the Designer is an infallible, supernatural deity, Casey is correct and bad design is predicted to not occur at all.

The problem is that the Discovery Institute explicitly states that intelligent design cannot identify whether or not the Designer is supernatural, thereby forcing them to promote pure ID over ID creationism. This works well from a defensive perspective, as they are now safe from the obvious “design flaws” in many organisms, but it has the undesirable effect of rendering their idea completely unscientific – it cannot make predictions and it cannot be falsified, two important properties that it lacks when compared to properly scientific hypotheses.

What this means is that ID proponents cannot use scientific discoveries about the functionality of “junk DNA” to support intelligent design while at the same time claiming that ID is not affected by the existence of suboptimal systems and structures in organisms. The fact that the Discovery Institute continues to make both claims is evidence that they are not applying rigorous thought to their own ideas.

The next time an ID proponent mentions either functional “junk DNA” or bad design, inform them about the conflicting nature of the two ideas, and see how they react.

Saturday Morning Miniblog Update – Extra Evolution!

Christmas and New Years got the better of me for the past two weeks, but I’m going to make it up to you with nothing but news stories about evolution. I do treat you well, don’t I?

- Prions capable of evolution (Now you have even more reason to be hysterically scared about prion diseases…)

- Even killer whales cannot escape the pull of evolution (Soon they’ll be evolving into the fabled human-eating niche!)

- Eight percent of the human genome is bornaviral in nature (This leads me to suspect that claims about junk DNA are founded in at least some truth, eh Discovery Institute?)

- More evidence against a “metabolism first” origin of life (Another interesting development – it’ll be good to see where this field goes in the next ten years.)

CB130: “Junk” DNA is not really junk

This is a post refuting part of the CreationWiki response to Talk.Origins’s “Index to Creationist Claims”. Click here for an introduction to this project. Quotes from CreationWiki are in red, while quotes from Talk.Origins are in blue.

Original Creationist Claim

So-called junk DNA is not really junk. Functions have been found for noncoding DNA which was previously thought to be junk, and we cannot be sure that the rest of the junk DNA is not functional as well.

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