Talk:Expelled: Leader's Guide

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On Mr Flew's comments

I really enjoy all the responses to the Expelled article, but I really don't think that this particular response does anything in regard to answering the Expelled article. The article says that he believes that DNA points to ID, and therefore he is a theist, and the response is that he definitely isn't Christian? That doesn't really help the Evolution argument or heard the ID one either, it's just purposefully ignoring the point, and I don't think this article needs to drop to that level. Just my opinion, will keep reading now :).

Missing space in title

The title is "Expelled:Leader's Guide" without a space after the colon. Was this intended to be a namespace? If not, maybe it's worth moving the article to "Expelled: Leader's Guide" (with the space)? --Tweenk (talk) 07:25, 21 March 2011 (UTC)

Yes, that's a mistake. Let me fix that for you.. DogP (talk) 18:19, 21 March 2011 (UTC)

I don't agree with the programmer argument

First of all a disclaimer. This is my first post here and it would be reasonable to assume I haven't a clue. Feel free/encouraged to point out this is this should of been posted at the bottom/on a different page/in a different topic/not at all. I thought the programmer argument in Expelled:_Leader's_Guide#The_Living_Cell was weak.

"We also observe that any computer programmer that hasn't already been fired liberally salts their code with comments explaining what the various subroutines do and what the variables are for.

One challenge to ID has always been: Show me the comments in the DNA before you claim someone (or thing) wrote it. "

Unfortunately at work a lot of our code base lacks good comments. It's just not true that people who don't comment get canned though I kind of wish it was. people are busy and the main purpose of comments is to explain to OTHER people whats going on. It's possible that god doesn't want people tampering with his supper optimized code, or wasn't thinking of others when he wrote it. Another problem with this argument is that comments are removed when the code is compiled from source. for those who don't know there are two different kinds of code, source code which is human or at least programmer readable(more readable anyway) and compiled code which is computer runnable. So it's possible that the source code or documentation exists but is written elsewhere. or that the so called junk DNA contains the comments but its in some kind of god language or something. I think I may have read that at least some of the junk dna had a function somewhere, but I forget. Finally its possible that god thought it was obvious what it did. For the time being I'm removing the sentences that I disagree with but feel free to put them back and slap me down/revert me explaining this isn't how we do things and/or I'm wrong.

NonPerson (talk) 14:55, 17 May 2014 (UTC)

It looks like your edit has survived long enough to stand a chance of staying. FWIW, I agree that "show me the comments!" is weak to the point of irrelevance. God, being omniscient and unique (by his own commandment) doesn't face the problem of "WTF was I thinking when I wrote that!?!??" I don't know enough about genetics to say anything substantial about "junk" DNA, but I can still wave my hands at how new facets of the way the code interacts epigenetically with the environment are still being discovered. Sprocket J Cogswell (talk) 01:30, 3 June 2014 (UTC)

The junk DNA argument is perilous

It is now a widely held view in molecular biology and genetics that the so-called "junk DNA" (or more technically non-coding DNA) actually isn't junk. Functions have already been ascribed to some of it, and new functions are regularly found.

A good review of the subject can be found here: http://robotics.stanford.edu/~serafim/CS374_2006/papers/mattick.pdf

I wouldn't try to claim that every base pair in our DNA has a use; certainly some of it it just a trail of viral DNA which has lost its ability to replicate, and no doubt some represents genes that have mutated and therefore no longer function (i.e. pseudo genes). But I wouldn't use the junk DNA argument, because every time a new function is found in non-coding DNA, the creationists will cite the paper as validating their argument. Marchino61 (talk) 05:47, 14 June 2015 (UTC)

I second this. I know that the ENCODE claim of an 80% functional genome is very controversial for a number of legitimate reasons, however many regions previously thought to be 'junk DNA' because of low (or no) sequence conservation are now known to either a) be human specific (harder to detect signatures of selection), b) exhibit VERY weak signs of selection in only certain functional domains) or c) exhibit conservation on other levels, such as secondary structure. A good example is provided by long noncoding RNAs, which generally show very little or no sequence conservation between species, yet repeatedly exhibit a conserved overall function. The term 'junk' was originally used to refer to transposable elements (TEs). TEs are DNA sequences which encode DNA signal patterns and proteins that facilitate their own duplication and reinsertion in a host genome; for this reason they've also been called genomic parasites. DNA derived from TEs makes up 45% to over 66% of the human genome.

Although there are many others, here is an open 2014 paper that reviews the contribution of transposable elements to the function of long noncoding RNAs:

http://rnajournal.cshlp.org/content/20/7/959.long

Another interesting paper that ties together ENCODE, transposable elements and the concept of junk DNA is here:

http://biophilosophy.ca/Publications/conceptual&empiricalchallenges.pdf

I'll add that there are other functions for 'junk DNA' that are not facilitated by any one sequence but nevertheless present a phenotype that can be acted on by natural selection. The size of a genome, for example, affects the amount of DNA that must be replicated before cell division and could conceivably affect the a) time and b) resources required for growth. Under this model the amount of filler DNA could have important implications for the fitness of an organism.

Further to the above, the term 'junk DNA' was initially only introduced in the 1980's because researchers studying transposable elements were getting a bit carried away in hypothesizing the importance of TEs in the evolution of regulatory regions and protein-coding genes in the human genome, without enough evidence. Old papers such as this and this suggested that the presence of TEs could be explained by selection on the 'parasitic' DNA sequences themselves, rather than some benefit to the host organism. The term stuck, and is mostly used these days as an introductory hook in papers that then proceed to demonstrate some function of TE-derived sequence. A mountain of evidence has recently shown that TEs contribute to the re-wiring and creation of novel coordinated gene regulatory networks, such as those partly responsibility for controlling pregnancy in humans.

From a more practical and rhetorical standpoint, I agree with Marchino61 that the term 'junk' provides an easy (if misguided and misleading) avenue of attack for ID supporters whenever previously unknown functionality is ascribed to some region of the genome. It's easy to see the 'junk' term becoming perceived as (incorrectly) analogous to the God of the gaps fallacy; creationists could see scientists as relying on an ever-shrinking pool of 'junk DNA', which decreases in size whenever a new discovery is made, to justify evolution by natural selection.

This is a particularly long edit since I'm a new user and wanted to justify my position. That being said, on the basis of Marchino61's and my comments I'm going to delete the sentence in question.

Junkdna (talk) 22:01, 28 July 2015 (UTC)

Artificial selection, Natural selection and Nazi eugenics

In the section titled What does it matter? Summary:, the following is used to rebut the assertions that Darwinian evolution provided a scientific justification for Nazi eugenic policies:

"If Hitler used Darwin’s "survival of the fittest" to justify eugenics, it was a misapplication of the theory. Evolution works by natural selection. Any action the Nazis took would not, by definition, be considered natural selection. In any case, evolutionary theory makes no judgements that would justify selective breeding of humans to eliminate large portions of the human gene pool. Evolutionary theory suggests that the larger the gene pool, the greater the chances of long term survival for any population."

There are a whole whack of problems with this rebuttal; I feel it should be removed or replaced. There is a much more direct response to claims that Hitler occasionally latched on to Darwinian theory to justify his actions, and it has already been alluded to on this page. In brief: "So what? The validity of the Theory of Evolution by Natural Selection has nothing to do with how certain groups of individuals apply its principles."

Let's break it down:

"Evolution works by natural selection. Any action the Nazis took would not, by definition, be considered natural selection."

I feel that this comment is much more interested in distancing the theory of evolution from the Nazis than it is in presenting an honest account of evolutionary science. In the context of this page, the term 'natural selection' is understood to be synonymous with the current scientific understanding of how new species arise and how the diversity of life came to exist over the course of evolutionary time. The rebuttal in question abruptly deviates from that interpretation, and instead adopts a highly specific definition of natural selection; namely, that 'natural selection' is distinct from 'artificial/human-driven' selection. Although it's unfortunate when trying to rebut the shallow arguments of creationists, artificial selection is only semantically different from natural selection. That is, whether it's humans or other 'external environmental factors' that are exerting it, a selective force exists which, through the inherited variation of progeny and survival of the fittest (ie Darwin's requirements), can promote change and speciation over time. It really doesn't matter where the selective force comes from, because under both natural and artificial selection any genomic mutations that are beneficial to the survival and propagation of the host organism will generally, barring stochastic forces, lead to its success. The core tenets of evolution don't care at all whether a selective force is provided by a human intellect or by other environmental factors; the same principles apply.

Consider a horrifying hypothetical example: the Nazis were successful in identifying a 'Jewish-ness' (or Polish-ness, or Slavic-ness, etc) gene or set of mutations and successfully murdered every individual carrying such markers. These mutations would be removed from the 'gene pool' in a similar way to those of a group of individuals who were especially susceptible to a particularly deadly virus, and, unless they arose again by chance, would no longer be present among members of our species. Why? Because of an external selective force that drastically reduced the fitness of those individuals carrying such genetic markers. Be sure to note: intellectually-driven intent is only incidental. Take a separate example: the Nazis follow one of their initial plans and deport all Jews to Madagascar, where they subsequently have no interactions with any other humans. This case is analogous to any number of reproductive barriers that have been shown to occur between newly emerging species (new mountain ranges, isolation on an island, genetic incompatibility resulting from a mutation, etc) and, according to modern evolutionary thought, could very well lead to the creation of a distinct, reproductively isolated 'Jewish' species after a considerable amount of evolutionary time. The fact that a human intellect drove such changes is irrelevant to the processes at work. By the way, I want to be explicitly clear: while there are certainly (relatively) very small differences between human populations, there is absolutely no evidence that such population-specific individual mutations affect behavior or culture in any sort of way that would ever appear on the moral compass of even the most ardent Nazi.

This is getting a bit long-winded, but my point is that you can't make a distinction between artificial and natural selection when discussing the role of evolution in the origin of diverse species. If you say that the Nazis' eugenic policies are NOT based on a "true" interpretation of Darwinian evolution, as is implied by the rebuttal in question, you may as well also declare that all of the studies which have experimentally demonstrated evolution over short time scales (using bacteria, flies, etc) provide NO valid evidence simply because humans designed and oversaw the studies. While you're at it, you could also claim that the outcomes of most practical applications of evolutionary theory, such as those used to mitigate antibiotic resistance, pesticide resistance or the adaptation of infectious organisms, exist in their own 'artificial' bubbles and in no way provide evidence for evolution.

The rest of the rebuttal/point in question is also problematic:

"In any case, evolutionary theory makes no judgements that would justify selective breeding of humans to eliminate large portions of the human gene pool. Evolutionary theory suggests that the larger the gene pool, the greater the chances of long term survival for any population."

Once again, at first this sounds nice and seemingly shows that the Nazis "just didn't understand real evolution!". The sentence also slightly implies that evolution DOES make judgements, just not ones that are in line with Nazi ideology. Evolution is only a process. It passes no judgement on any ideology including Nazism, and unfortunately it's a process that could absolutely be used to further a nefarious agenda. Also, contrary to the provided rebuttal, it's dead simple to come up with a species-level justification for removing large numbers of individuals from a population. Take the example of a 'cheater' mutation: a mutation which causes the carrier to be more successful (selected for) at the expense of other individuals of its species. In a system where every organism is working together for a common good that provides immense benefit to the entire species, a cheater can receive the overall benefit while not directly contributing. As a result, the cheater individual can spend more resources on its own reproduction than other members of its species. Once again barring random effects like genetic drift, the cheater mutation will become more and more common in the population until there aren't enough 'selfless' individuals for the 'common good' to be maintained. It would ABSOLUTELY be to the benefit of the entire species for some force to eliminate all of the 'cheater' mutations, even if they were relatively common in the population. In this hypothetical situation, a larger gene pool doesn't offset the collective cost of allowing a cheater mutation to continue propagating in the population. From the (morally inconsistent and horrific) Nazi point of view, Jewish and other "undesirable" peoples were seen as carriers of a 'cheater' mutation which worked against the betterment and success of a humanity best led by an 'Aryan race'. To use evolutionary terminology and (momentarily) adopt the regressive, simplified and frequently scientifically appalling view of the Nazis, humanity as a collective system of generally 'altruistic' (ie serving an arbitrary 'common good') individuals would have been more fit and successful if certain 'unfit/bad' genes (and the Jewish individuals carrying them) were eliminated from the species.

To be frank, this rebutting point relies on flawed logic. If someone said that all of the theories governing nuclear physics were wrong because nukes have killed hundreds of thousands of innocents, an (incorrect) equivalent to the point in question might be to claim that: "No, theories of physics are entirely correct because mutually-assured destruction has actually led to a massive decrease in both wars and human lives lost!". The moral dimensions of the APPLICATION of a scientific theory say NOTHING about the validity of the theory itself.

In short, Hitler did not 'misapply' the theory of evolution. If you accept his flawed foundations, he even got the gist of it. A much better rebuttal might point out the fact that terms such as 'inferior' and (in this context) 'unfit' are moral considerations by humans that say nothing about how species arise or change over time. Since this is, after all, RationalWiki, if we want a witty quip we could point out the opposite side of the moral coin: evolutionary principles have facilitated the iterative development of novel cancer-treating drugs, have led to important AI and software-design paradigms, have helped us feed millions by circumventing the adaptation of plant parasites to certain pesticides, and have led to policies that continue to prevent the global spread of bacteria which are immune to all antibiotics.

Although it might not be as palatable a rebuttal to ID-proponents/creationists, you could also point out that there are many, many traits which would be considered morally 'naughty' but which nevertheless likely increase the fitness of an individual. It's probably not going to convince any creationists, but the honest truth is that ANY mutation which provides a net benefit to the individual will be selected for. To be blunt, this arguably includes morally-charged concepts that ("even with God") continue to be abused by many humans with frightening frequency such as: rape, murder, theft, siblicide, infidelity, tribalism, pretty much all logical fallacies, and yes, even genocide. Don't get me wrong; there are areas of the human experience that simply cannot generate the falsifiable hypotheses required by science, most of which involve concepts that seem to be beyond human comprehension. Evolution by natural selection is not one of these. In fact, the current understanding of evolution can in its entirety be applied to anything... from the rocks and the trees to the birds in the sky.

This comment sure ran on... anyway, I'll leave it here for a while for discussion and if nobody objects I'll change the Hitler-evolution summary rebuttal in a few weeks.

Junkdna (talk) 03:50, 29 July 2015 (UTC)

On 'Mutations: not a problem'.

Although a good argument against the argument posed by Expelled, it should be noted that the argument does not adress much more compelling evidence against the original point. Maybe it should be noted that modern understanding of molecular evolution accounts for neutral mutations, slightly deleterious mutations and soft selection on coding DNA sequences.

Also in general, there is a 'random' component of evolution, genetic drift, that should be at least mentioned. Hiding facts is as bad as telling lies. ^{— Unsigned, by: User:201.172.3.194 / talk / contribs}