Comment on The End of “Junk DNA”? by Sean Pitman.

@pauluc:

Nice to see you are back. I had hoped you might have thought a little more about confirmational bias in selection of your sources. In reading your turtles book I was [struck by] the sentiment expressed again here that you as a literal creationist had anticipated the function of the whole of the genome well before people like John Mattick had provided experimental evidence for the role of non-coding RNA? This is really quite a bold claim but I cant seem to find any reference to your prescient publications on this topic.

A working draft of the human genome was announced in 2000 but our complete genome wasn’t finished until 2003. Before this time, most life scientists argued, since the 1960s, that non-coding DNA was largely functionless – evolutionary remnants that still tagged along with the relatively rare functional genes within our genome. In 1995, Scientific American plainly expounded that under the Neo-Darwinian view, “[t]hese regions have traditionally been regarded as useless accumulations of material from millions of years of evolution.” The view that non-coding DNA is truly “junk DNA” has been adamantly promoted by most at Talk.Origins for years. Certainly by the time I started posting on Talk.Origins in 2001 this view was the common paradigm.

In contrast, I have been personally writing about the functionality of pseudogenes and “junk DNA” since 2001 – on my website and in discussion forums. For example, here is a portion of a discussion I had in 2002 in google.groups:

“We are still very limited in our knowledge about how the genome actually works even though we have sequenced the entire human genome. We are finding out that much of what we previously referred to as “junk DNA” actually has some pretty impressive functions. Just because a portion of DNA does not code for a protein does not mean that it has no function or that it is some remnant of past evolutionary baggage or trials and errors. Even some so-called “pseudogenes” are now being found to in fact have certain important functions… such as gene switching or gene regulation. This is almost reminiscent of the vestigial organ arguments of the past. What used to be thought of as functionless remnants of evolutionary heritage, are now known to have important if not vital functions in the present state of the creature. As the number of “vestigial” organs are shrinking, so are the number of “non-functional” genetic sequences.”

http://naturalselection.0catch.com/Files/Pseudogenes.html

Sean Pitman

Yet, at this point in time (in 2002), most scientists still held to the view that the vast majority of non-coding DNA was not functional. For example, in 2001 Stephen J. Gould wrote:

Our 30,000 genes make up only 1 percent or so of our total genome. The rest — including bacterial immigrants and other pieces that can replicate and move — originate more as accidents of history than as predictable necessities of physical laws. Moreover, these noncoding regions, disrespectfully called ‘junk DNA,’ also build a pool of potential for future use that, more than any other factor, may establish any lineage’s capacity for further evolutionary increase in complexity (Gould 2001).

Clearly, Gould was mistaken. The non-functionality of “junk DNA” was also predicted by Susumu Ohno (1972), Richard Dawkins (1976), Crick and Orgel (1980), Pagel and Johnstone (1992), and Ken Miller (1994), based on evolutionary presuppositions. In contrast, on teleological grounds, Michael Denton (1986, 1998), Michael Behe (1996), John West (1998), William Dembski (1998), Richard Hirsch (2000), and Jonathan Wells (2004) predicted that “junk DNA” would be found to be functional.

As far back as 1994, pro-ID scientist and Discovery Institute fellow Forrest Mims had warned in a letter to Science against assuming that ‘junk’ DNA was ‘useless.'” Science wouldn’t print Mims’ letter, but soon thereafter, in 1998, leading ID theorist William Dembski repeated this sentiment in First Things:

[Intelligent] design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how “non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development.” Design encourages scientists to look for function where evolution discourages it.

(William Dembski, “Intelligent Science and Design,” First Things, Vol. 86:21-27 (October 1998))

Here are a few more recent references:

Casey Luskin (2007):
http://www.ideacenter.org/contentmgr/showdetails.php/id/1437

Tim Standish (2002):
http://star.tau.ac.il/~eshel/Bio_complexity/12.Gene%20Networks/Introns-JunkDNA-summary.pdf

Linda Walkup (2000)
http://creation.com/junk-dna-evolutionary-discards-or-gods-tools

On another issue that you cite again here is the issue of mutation rates. I am curious if you have read the Kong paper in [the journal Science]

http://www.ncbi.nlm.nih.gov/pubmed/22914163

on the effects of paternal age on transmitted mutations to offspring. Obviously this has implications for the putative antedeluvian populations and the genetic front loading of the population although unfortunately any front loading by these mechansisms would have been largely if not entirely wiped out in the genetic bottleneck at the flood.

If you read the paper you will see that the number of mutations increases by 2 for every year of paternal age from a baseline in their data of 29.7 years. On an exponential model the mutation rate doubles for every 16.5 years of paternal age.

According to genesis 5 and the patriarchal ages the average paternal age for first child was 155.6 and the text implies they were reproductively active on the average for another 706.9 years.

I don’t see this “implied” by the text. The Bible simply doesn’t say when the antediluvians became too old to have children.

Using Kongs calculation from the direct genomic sequencing of 78 icelandic families what can we determine?

From cell division to cell division, the error rate for DNA polymerase combined with other repair enzymes is about 1 mistake or mutation in 1 billion base pairs copied (for many but not all of the cell types in our bodies). In men, there is approximately one spermatic stem cell division every 16 days (about 23 divisions per year). This implies a yearly mutation rate in male gametes of around (3 x 23) or 69 mutations per year. Yet, we know that the overall human nucleotide mutation rate (SNPs) is less than 100 per generation. Obviously, the mutation rate for gamete production is significantly reduced relative to other types of cells within the body – probably due to enhanced correction rates for mutations due to the error rate of DNA polymerase.

In any case, it seems like the gamete mutation rate would still be related to copy number (the number of stem cell divisions), and therefore would most likely be a linearly increasing mutation rate as copy numbers increased. In other words, if the average increase in gamete mutations is 2 per year (as several references seem to suggest), it seems to me like this increase would stay fairly steady with age – i.e., that it would not follow an exponential curve. As I look as the graphs provided by the article you reference, graphs comparing mutation rates to paternal age, I don’t see that there is evidence to support an exponential increase in the mutation rate with age. The data just as easily supports a linear model; a model that seems to be more consistent with known sources of mutations in germ cells.

According to the linear model for increasing mutations, the mutation rate for progeny of the patriarchs was between 3 (3.09E-8 per nucleotide) and 15 (14.875E-8) times the current rate (1.2E-8). Using their [esponential] model the rates are up to 273,276 per nucleotide per generation, a rate 2.27E13 more than the current rate. Clearly this is absurd but would certainly be in the range of a genetic meltdown anticipated by Sanford.

Given the linear model (which I agree with) an increased rate of 2 mutations per year, starting at the age of 30 years, works out to less than 1600 mutations at the age of 800 years. This is in line with the yearly average mutation rate we humans currently suffer per generation (about 2-3 mutations per year on average or between 50-100 SNPs per generation). I really don’t see the problem here unless one tries to invoke the exponential model.

How does one respond to this sort of data? At the level of the science; with very old age of paternity it is likely that the linear model is an underestimate while the exponential model may fit the data only for conventional ages but if you take literally the ages of the patriachs and construct some mechanistic model one must assume some sort of sigmoidal distribution as nucleotide substitution must reach some point of saturation well below a subtitution per nucleotide per generation.

Again, I don’t see any reason to invoke the exponential model. There may be a slight variance from the linear model with age, but I don’t think it would be enough to significantly outpace current yearly mutation rates for the human genome.

The bigger question is do we even take the science seriously? As I have said before I suspect you do not. If we do, what do we do with the account of the patriarchal ages let alone the similar ages of the Sumerian kings.

I take science, and even the claims of modern scientists (not necessarily the same thing as “science”), very seriously. However, many of the extrapolations of mainstream scientists are very tenuous or simply untenable given the empirical evidence currently in hand. I personally find the Biblical account to be far more in line with the weight of scientific/empirical evidence that I personally understand.

As far as very long-lived races are concerned, this is not beyond rational consideration or scientific tenability given that there are many different species that have “negligible senescence” (that do not get old with age). Examples include certain kinds of carp or lobsters or turtles which do not lose very much if any vitality or virility with age. Perhaps humans used to be like this as well? – especially given the fact that our genomes are degenerating over time?

As already discussed, we are headed toward an eventual genetic meltdown. We are not in meltdown mode now, of course, but we are clearly headed downhill genetically and will eventually reach the tipping point. It is science that clearly shows a decaying human genome with implications that it could have been much better, with significantly enhanced features of health, longevity, and overall vitality, thousands of years ago as compared to today – as the Bible claims.

Do we, as you seem want to do, add another layer of exceptionalism (ie miraculous God of the gaps reasoning for understanding of the natural world) as you have done for the question of front loading and genetic bottlenecks for the anteluvian world and repopulation from a breadding pair.

I’m sorry, but I was under the impression that it was you who wanted to invoke God to explain such things – not me. I’ve never invoked God to explain survival after genetic bottlenecks or the current state of affairs starting with a single breeding pair. The available scientific evidence is perfectly consistent with the Biblical account of such a bottleneck after the Noachian Flood as well as the decline of genetic quality of all slowly reproducing gene pools since their original creation. You’re the one who is trying to say that this is not possible outside of a Divine miracle, not me. God-like intelligence is only needed to explain the original origin of life and its diversity – the original “front-loading” if you please. And, I don’t see that you’ve brought anything else to the table that would require God to directly interfere with the natural course of things . . . the natural inevitable decay and degeneration of all slowly reproducing gene pools from their original idealic state.

For many of us, including I suspect the scientists at la sierra who you malign yet again in this posting, we are happy to accept the evidences of science but would see the action of God not in our ignorance as the explanation of the inexplicable in the natural world but in the action of Jesus Christ the incarnate God who is the basis of our faith.

It is the Bible that testifies of Jesus Christ, His nature and origin. Undermine the Bible’s credibility, and you undermine any rational faith you may have in the story of Jesus and any of His claims. You can’t rationally have one without the other. They go hand-in-hand. Certainly Jesus Himself saw it this way. He took the Scriptures seriously – to include the Genesis account of origins. He believed the stories of Genesis and referenced them as literally true. He even claimed to have personally witnessed prehistoric events. Do you believe Him or not?

Sean Pitman
www.DetectingDesign.com

Sean Pitman Also Commented

Recent Comments by Sean Pitman