When "Junk DNA" Isn't Junk: Farewell to a Darwinist Standard Response
In the Darwinist repertoire, a standard response to evidence of design in the genome is to point to the existence of “junk DNA.” What is it doing there, if purposeful design really is detectable in the history of life’s development? Of course this assumes that the “junk” really is junk. That assumption has been cast increasingly into doubt. New research just out in the journal Nature Genetics finds evidence that genetic elements previously thought of as rubbish are anything but that. The research describes tiny strands of RNA, previously thought to be junk, that now turn out to play a role in gene expression. Another finding by Dr. Geoff Faulkner shows that “retrotransposons,” a further variety of “junk” as the dogma previously taught, play a similar role.
Nearly half of the mammalian genome (less than 45 percent) is comprised of DNA sequences thought for decades to be but evolutionary flotsam and jetsam or junk: retrotransposons. Found along every one of our chromosomes, retrotransposons mobilize within our cells via RNA copies, copies that are then converted into DNA and afterward pasted into different DNA sites. To be sure, the vast majority of these “jumping gene” duplicates, well over a million elements, appear to be little more than pseudogenes, defective images of master templates that merely drift by mutations into a phylogenetic oblivion.
Retrotransposons appear to fit the neo-Darwinian story perfectly. First, the master templates of these elements seem to serve no other purpose than to promote their own replication at the expense of the cell, and so, by the criteria of Richard Dawkins’s 1976 book The Selfish Gene, retrotransposons are selfish genes par excellence. Second, the DNA progeny of such “endogenous viruses” are without a doubt marred in various ways, as just mentioned. Relative to the original, in other words, they are junk. Third, a retrotransposon inserted into a chromosome can disrupt normal gene functions, and mutations due to these sequences have long been detected. Fourth, only a comparative few retrotransposons are conserved across different groups of mammals, with most of the DNA families being restricted to certain families, genera, or even species. Humans and mice as well as mice and rats can readily be separated solely on the basis of their retrotransposon profiles. So the bulk of these sequences do not merit being retained by natural selection.
With such facts at hand, it is no wonder that retrotransposons and other “non-coding” DNAs are part of Exhibit A on the side of the neo-Darwinian prosecution, over and against the intelligent design defense.
But there have always been big holes in this tale of selfish, junk DNA. We have known since the late 1980s that retrotransposons are distributed non-randomly along chromosomes. Even though humans and mice and rats have different families of these sequences — ultimately a reflection, according to neo-Darwinists, of randomness — the linear pattern of placement of the elements is uncannily similar. Likewise, data accumulated throughout the ’80s and ’90s which indicated that normal gene regulation can be controlled by pieces of such mobile DNA. Evidence for other diverse regulatory roles of retrotransposons has also continued to mount till the present.
But it wasn’t until recently that we learned just how extensive is the informational impact of retrotransposons on the mammalian genome. The recent study by Geoffrey Faulkner et al. ("The regulated retrotransposon transcriptome of mammalian cells,") is only the latest. Using the RNA expression profiles of the human and mouse genomes as a backdrop, a number of key facts were uncovered. For one thing, tens to hundreds of thousands of transcription start sites — the beginning points of RNA transcripts — occur in retrotransposons. According to the data they gathered, anywhere from 6 to 30 percent of RNAs in the two species arise from repetitive (aka “junk”) DNA. For another, elements that reside in or near protein-coding genes provide alternative regions to initiate transcription, many previously unknown, and they allow for the production of various non-translated RNAs. The “start RNA production” signals conveyed by retrotransposons such as the mouse-specific VL30 retrovirus-like sequences are also markedly tissue-specific. Altogether, the results point to retrotransposons being “intrinsic components of the transcription forest regions of the genome” (Faulkner et al., 2009).
This is all rather awkward for the Darwinian side, obviously. Another standard weapon in their armory is to charge intelligent-design theorists with making a “God of the gaps” argument, where gaps in scientific knowledge are assumed to be evidence of design. The reality is that the case for Darwinian evolution is much more reasonably shown to depend on gaps — in our knowledge of what “junk DNA” does, for one thing. Hence a sobriquet for the view that evolutionists are saddled with defending: “Darwin of the gaps.”
Posted by Richard Sternberg on April 28, 2009 8:20 AM Permalink
当“垃圾DNA ”不是垃圾：永别了标准响应
在Darwinist曲目，一个标准的反应证明了设计中的基因组是指出存在的“垃圾DNA ” 。做什么是有，如果有目的的设计的确是探测在生命的历史的发展？当然这个假设的“垃圾”真的是垃圾。这种假设一直演员越来越令人怀疑。新的研究只是在自然遗传学杂志上发现的证据表明，遗传因素以前认为是垃圾的东西，但。这项研究描述了微小的RNA链，以前认为是垃圾，现在变成中发挥作用的基因表达。另一项调查结果博士杰夫福克纳表明， “反转录转座子” ，进一步各种各样的“垃圾”的教条以前任教，发挥类似的作用。将近一半的哺乳动物的基因组（小于百分之四十五）组成的DNA序列认为是几十年来，但进化废料和废弃的货物或垃圾：反转录转座子。沿途发现的每一个染色体，反转录转座子动员通过我们的细胞内RNA的拷贝，复制，然后转换成DNA和后粘贴到不同的DNA的网站。可以肯定的是，绝大多数的这些“跳跃基因”的重复，以及超过100万的内容，似乎是多一点的假基因，有缺陷图像的主模板，只是漂移的突变成一个系统发育遗忘。反转录转座子出现以适应新达尔文的故事完美。首先，主模板，这些内容似乎没有任何其他目的，而不是促进其自身复制为代价的细胞，因此，由标准的道金斯1976年的书自私的基因，反转录转座子是自私的基因出类拔萃。第二，cellence 。第二，cellence 。其次， DNA的后代，这种被称为“内源性病毒”是毫无疑问破坏以各种方式，如刚才提到的。相对原来的，换句话说，他们是垃圾。第三，座子插入染色体可能破坏正常的基因功能，基因突变，由于这些序列早就发现。第四，只有很少的反转录转座子是比较保守的不同群体的哺乳动物，其中大多数家庭的DNA受到限制某些科，属，甚至物种。人类和小鼠以及小鼠和大鼠很容易分离完全根据自己的座子概况。因此，大量的这些序列不值得保留的自然选择。有了这样的事实在眼前，这是毫不奇怪的反转录转座子和其他“非编码”指定的国家主管部门的一部分，展出的一方新达尔文起诉，并针对智能设计防御。但是，一直存在很大漏洞，这个故事的自私，垃圾DNA 。我们都知道自1980年代后期以来的反转录转座子分布非随机沿着染色体。虽然人类和小鼠和大鼠有不同的家庭，这些序列-最终反映，根据新Darwinists ，随机性-线性模式安置的内容是准确的相似。同样，积累的数据在整个八十年代和九十年代这表明正常的基因调控可以控制件，例如移动的DNA 。其他不同证据的监管作用的反转录转座子也继续挂载到本。但直到最近，我们的教训是多么广泛的信息影响的反转录转座子基因的哺乳动物。最近的研究杰弗里福克纳等人。 （ “管制座子的哺乳动物细胞转录” ）不过是最近的。利用RNA表达概况的人类和小鼠的基因组作为一个背景下，在个人资料的人类和小鼠的基因组作为一个背景下，é最新。利用RNA的表达é最新。利用RNA表达概况的人类和小鼠的基因组作为一个背景下，一些关键的事实被揭露。一方面，数万数以十万计的转录起始站点-点开始的RNA转录-发生在反转录转座子。根据他们收集的数据，时间从6至百分之三十的RNA在这两个物种的产生重复（又名“垃圾” ）的DNA 。另一方面，内容，或住在附近的蛋白编码基因提供替代地区发起转录，许多以前未知的，他们能够生产各种非翻译的RNA 。 “开始的RNA生产”信号传达的反转录转座子，如鼠标的具体VL30反转录病毒样序列也明显组织特异性。总之，结果指出，反转录转座子的“内在的组成部分转录森林区域的基因组” （福克纳等人。 ， 2009年） 。这是相当尴尬的达尔文方面，明显。另一个标准武器的军械库是负责智能设计理论的一个“上帝的差距”的论调，在科学知识方面的差距是假设的证据的设计。现实情况是，案件的达尔文进化更合理地表明取决于差距-在我们的知识是什么“垃圾DNA ”不，为一件事。因此，绰号的观点，即evolutionists是背负着卫冕： “达尔文的差距。 ”发布者理查德斯特恩伯格关于2009年4月28日上午8时20 固定
