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Jonathan Wells on Darwinism, Science, and Junk DNA

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Jonathan Wells

On November 5, I posted a response to people who falsely claim that I set out to oppose Darwinism on orders from Reverend Sun Myung Moon. Since then, many comments have been posted—some of them critical of my book, The Myth of Junk DNA. Unfortunately, other commitments prevent me from responding to every detail (so many critics, so little time!). So I have selected some representative comments posted by two people using the pseudonyms “Gregory” and “paulmc.”

First, “Gregory” asked how many biologists I think are “Darwinists.” In my original post, I wrote:

By “Darwinism,” I mean the claim that all living things are descended from one or a few common ancestors, modified solely by unguided natural processes such as variation and selection. For the sake of brevity, I use the term here also to include Neo-Darwinism, which attributes new variations to genetic mutations.

By “Darwinists,” then, I mean people who subscribe to that view. Having worked in close proximity with biologists for over two decades, I can confidently say that most of them—at least in the U.S.—are Darwinists in this sense.

“Gregory” also wrote that “without ‘doing science,’ Jonathan Wells personally concluded ‘evident design’ in ‘the mountains of Mendocino county.’ Thus, the argument that ‘intelligent design is a purely scientific pursuit’ is obviously untrue.” I’m not sure what “Gregory” means here by a “purely scientific pursuit.” Intelligent design (ID) holds that we can infer from evidence in nature that some features of the world, including some features of living things, are better explained by an intelligent cause than by unguided natural process such as mutation and selection. Unlike creationism, ID does not start with the Bible or religious doctrines.

So if “science” means making inferences from evidence in nature—as opposed to inventing naturalistic explanations for everything we see (as materialistic philosophy would have us do)—then ID is science.

Second, “paulmc” wrote that “there are a number of strong lines of evidence that suggest junk DNA comprises a majority of the human genome.” The lines of evidence cited by “paulmc” included (1) mutational (genetic) load, (2) lack of sequence conservation, and (3) a report that “putative junk” has been removed from mice “with no observable effects.” In addition, (4) “paulmc” wrote that “there is an active other side to the debate” about pervasive transcription. I’ll address these four points in order.

Before I start, however, I’d like to say that I’m not particularly interested in debates over what percentage of our genome is currently known to be functional. Whatever the current percentage might be, it is increasing every week as new discoveries are reported—and such discoveries will probably continue into the indefinite future. So people who claim that most of our DNA is junk, and that this is evidence for unguided evolution and evidence against ID, are making a “Darwin of the gaps” argument that faces the inevitable prospect of having to retreat in the face of new discoveries.

Now, to the points raised by “paulmc”:

(1) Mutational Load. In 1972, biologist Susumu Ohno (one of the first to use the term “junk DNA”) estimated that humans and mice have a 1 in 100,000 chance per generation of suffering a harmful mutation. Biologists had already discovered that only about 2% of our DNA codes for proteins; Ohno suggested that if the percentage were any higher we would accumulate an “unbearably heavy genetic load” from harmful mutations in our protein-coding DNA. His reasoning provided a theoretical justification for the claim that the vast majority of our genome is functionless junk—what Ohno called “the remains of nature’s experiments which failed”—and that this junk bears most of our mutational load.

According to “paulmc”, this is the first of “a number of strong lines of evidence that suggest junk DNA comprises a majority of the human genome.” But Ohno’s claim was a theoretical one, based on various assumptions about how often spontaneous mutations occur and how they affect the genome.

As of last year, however, the accurate determination of mutation rates was still controversial. According to a 2010 paper:

The rate of spontaneous mutation in natural populations is a fundamental parameter for many evolutionary phenomena. Because the rate of mutation is generally low, most of what is currently known about mutation has been obtained through indirect, complex and imprecise methodological approaches.

Furthermore, genomes are more complex and integrated than Ohno realized, so the effects of mutations are not as straightforward as he thought. As another 2010 paper put it,

Recent studies in D. melanogaster have revealed unexpectedly complex genetic architectures of many quantitative traits, with large numbers of pleiotropic genes and alleles with sex-, environment- and genetic background-specific effects.

In other words, the first line of evidence cited by “paulmc” is not evidence at all, but a 40-year-old theoretical prediction based on questionable assumptions. The proper way to reason scientifically is not “Ohno predicted theoretically that the vast majority of our DNA is junk, therefore it is,” but “If much of our non-protein-coding DNA turns out to be functional, then Ohno’s theoretical prediction was wrong.”

(2) Sequence Conservation. According to evolutionary theory, if two lineages diverge from a common ancestor that possesses regions of non-protein-coding DNA, and those regions are non-functional, then they will accumulate random mutations that are not weeded out by natural selection. Many generations later, the corresponding non-protein coding regions in the two descendant lineages will be very different. On the other hand, if the original non-protein-coding DNA was functional, then natural selection will tend to weed out mutations affecting that function. Evolution of the functional regions will be “constrained,” and many generations later the sequences in the two descendant lineages will still be similar, or “conserved.”

As “paulmc” pointed out , however, many regions of non-protein-coding DNA appear to “evolve without evidence of this constraint;” their sequences are not conserved. According to “paulmc,” this “implies that changes to these sequences do not affect fitness… we expect that for them to be functional they need some degree of evolutionary constraint,” and the absence of such constraint points to their “being putatively junk.”

Not so. Although sequence conservation in divergent organisms suggests function, the absence of sequence conservation does not indicate lack of function. Indeed, according to modern Darwinian theory, species diverge because of mutational changes in their functional DNA. Obviously, if such DNA were constrained, then evolution could not occur.

In 2006 and 2007, two teams of scientists found that certain non-protein-coding regions that are highly conserved in vertebrates (suggesting function) are dramatically unconserved between humans and chimps (suggesting… rapid evolution!). More specifically, one of the teams showed that one unconserved region contains an RNAcoding segment involved in human brain development.

Furthermore, the analysis by “paulmc” assumes that the only thing that matters in nonprotein-coding DNA is its nucleotide sequence. This assumption is unwarranted. As I pointed out in Chapter Seven of my book, non-protein-coding DNA can function in ways that are largely independent of its precise nucleotide sequence. So absence of sequence conservation does not constitute evidence against functionality.

(3) Mice without “junk” DNA. In 2004, Edward Rubin] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome—and that they could “see no effect in them.”

But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler said said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued.

In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other
circumstances.

(4) Pervasive transcription. After 2000, the results of genome-sequencing projects suggested that much of the mammalian genome—including much of the 98% that does not code for proteins—is transcribed into RNA. Scientists working on one project reported in 2007 that preliminary data provided “convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts.”

Since an organism struggling to survive would presumably not waste its resources producing large amounts of useless RNA, this widespread transcription suggested to many biologists that much non-protein-coding DNA is probably functional. In 2010, four University of Toronto  researchers published an article concluding that “the genome is not as pervasively transcribed as previously reported.” Yet the Toronto researchers had biased their sample by eliminating repetitive sequences with a software program called RepeatMasker, the official description of which states: “On average, almost 50% of a human genomic DNA sequence currently will be masked by the program.” In the fraction that remained, the Toronto researchers based their results “primarily on analysis of PolyA+ enriched RNA”—sequences that have a long tail containing many adenines. Yet molecular biologists had already reported in 2005 that RNA transcripts lacking the long tail are twice as abundant in humans as PolyA+ transcripts.

In other words, the Toronto researchers not only excluded half of the human genome with RepeatMasker, but they also ignored two thirds of the RNA in the remaining half. It is no wonder that they found fewer transcripts than had been found by the hundreds of other scientists studying the human genome. The Toronto group’s results were disputed in 2010 by an international team of eleven scientists, and the group’s flawed methodology was sharply criticized in 2011 by another international team of seventeen scientists.

So “paulmc” was technically but trivially correct in writing that there are two sides to the debate over pervasive transcription. There are also at least two sides to the larger debate over the functionality of non-protein-coding DNA. But I leave it to open-minded readers of The Myth of Junk DNA to decide whether “paulmc” was correct in claiming that “the science at the moment really does fall on one side of this: large amounts of putative junk exist in the human genome.”

Oh, one last thing: “paulmc” referred to an online review  of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.

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Comments
GilDodgen @ #3 'Darwinists are chasing a rainbow in their attempt to explain away engineering with a process (randomness) that is the antithesis of what is required to produce the result in question.' GilDodgen, I wonder if Darwinists believe that randomness reverse engineered human artifacts (created by their own naive realist, good selves, of course), and then travelled back in time, to make it look as if IT had created everything; when it had actually cribbed the designs from themselves? The promissory note finally made good! More food for thought. It would make a nice Just So Story. Or is it too Byzantine even for their corkscrew minds, I wonder?Axel
April 20, 2015
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Bornagain, Could you point me to Jon Wells' you-tube video where he shows that once a cell membrane is punctured, the cell dies regardless of all the other conditions favourable to life (basically a counter-abiogenesis demonstration). This was called something like "10 minutes proof of ID" if I remember rightly. Thanks.Eugene S
April 22, 2012
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Me too: Yeah, yeah, enough with "junk DNA" already. Relax this is a different angle. In Genetic/ Evolutionary Algorithms and My Front-Loaded Evolution, I said:
So with my idea of front-loaded evolution we would have the initial conditions, the required resources, the specified result (ie what you are trying to accomplish) and then the algorithms to make it all happen. (bold added)
As with Richard's Dawkins "weasel" program, which took scrambled letters and having the whole alphabet as its resource, was able to create a pre-specified target sentence, front-loaded evolution would be able to take truly non-functioning DNA sequences and splice them together to meet some pre-specified function. That is why front-loaded evolution does NOT need to have all the alleles present as evotards so wrongly claim. All front-loaded evolution requires is that the future design be obtainable through the present design. In this case the alleged "junk" is just stock to select from, ie "the required resources".Joe
December 2, 2011
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In case any of you guys are interested, I am blogging fuller discussions about junk DNA elsewhere.paulmc
December 1, 2011
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The takeaway headline from Goodwin’s research seems to be, as expressed in the summary title “there is more to evolutionary biology than genes.” Indeed. That is part of my point.
That's quite a stretch. Yours and Goodwin's points are almost opposites: you have claimed several times that there is a much greater degree of genetic determinism than is currently known to exist - indeed the types of genetic controls you expect are undiscovered in the genome would be described as a gene class were they to exist; Goodwin, on the other hand, de-emphasises the role of genetics in favour of a structuralist approach as he believes the genome had a far less prominent role in the generation of form than do neoDarwinists. See his book chapter discussion with Dawkins - web text version here.
We have discovered that a portion of DNA consists of genes that code for proteins. Based on that, many staunch materialists have proclaimed that the rest is junk. Little by little, other functions are being discovered, yet the junk DNA myth persists.
Are we back to this again? Junk DNA is a scientific inference, not some empty/ignorant assertion. If you want to claim the death of junk DNA from either newly discovered classes of RNA genes, new miRNAs or from other functions then you need to provide the numbers for your case (an argument I've made on this blog and elsewhere in response to Wells). While there has been lots of talk disparaging the concept of junk DNA here, no one has yet outlined a legitimate basis for referring to junk DNA as a 'myth'. Nor does the inference of junk DNA have any logical connection with a materialist viewpoint. I have outlined parts of the case for junk DNA so many times above and in the previous thread that spawned this one, that it beggars belief that the same, 'argument' is still getting recycled when those points have still not been answered.
Goodwin’s research relates to a single-celled organism that has a repeating-patterned, circular shape.
Goodwin says this: "In Acetabularia the spherical zygote has to break out of its simplicity into ordered complexity of form. The technical term to describe the transition from a state of higher symmetry (lower complexity) to one of lower symmetry (higher complexity) is bifurcation." So it is not a matter of it being a simple, circular shape. The simple interactions between calcium concentration and the cytoskeleton result in complex breaking of symmetries - the whorls and end cap.
Simple example: is there something about cartilage cells that cause them to physically arrange in the form of a nose? The answer is clearly no, because we know of other arrangements that exist. Is there anything about chemistry and physics that causes your front tooth to take the shape that it does? No. Because we can look and see that other shapes are possible.
I completely agree that there are genetic components that influence cartilage and bone morhpology, tooth morphology and all manner of other phenotypes. These genetic components contribute to the differentiation between and within species in phenotypes. However, there is a giant gulf between that and assuming such differentiation is the result of "an incredible degree of carefully orchestrated and controlled processes" - with such tight and specified control that you seem to believe they make junk DNA a myth.paulmc
November 19, 2011
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I am beginning to note a certain pattern regarding the semiotic argument.Upright BiPed
November 18, 2011
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Okay well. Looks like we won't be discussing any evidence today. I suppose asking someone to substantiate their remarks is off the table. I guess I should join the deniers and talk about socio-politics and religious angst instead. ;)Upright BiPed
November 18, 2011
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paulmc, I read the chapter of Goodwin's work you linked to. Thanks for the link. (Haven't had time to listen to the TED talk, but perhaps after the holidays.) First of all, it looks like Goodwin was doing some interesting science and I hope he is still at it or that someone has picked up the baton, because there are certainly worthwhile things to research in this area. As it relates to my point, however, I would say Goodwin's research is the exception that proves the rule. Just a couple things that jumped out at me from reading about his research: - The takeaway headline from Goodwin's research seems to be, as expressed in the summary title "there is more to evolutionary biology than genes." Indeed. That is part of my point. We have discovered that a portion of DNA consists of genes that code for proteins. Based on that, many staunch materialists have proclaimed that the rest is junk. Little by little, other functions are being discovered, yet the junk DNA myth persists. I agree, there is definitely more to biology than genes. - Goodwin's research relates to a single-celled organism that has a repeating-patterned, circular shape. That is precisely the kind of shape that natural chemical affinities are good at making. That a particular single-celled organism would make use of natural chemical/physical affinities between molecules in making its shape is interesting, but is hardly relevant to the vast majority of other organisms that do not have such simple, repeating shapes. - Even with the simple shape that acetabularia acetabulum enjoys, it is not clear from the article that this is really an example of "self-organization". Specifically, the organism still has a suite of proteins that are necessary for construction and, apparently, the organism has some kind of regulation over the amount and speed of construction, as well as its ultimate size (why does it stop growing when it does, for example?). - Even if it were the case (which is not at all clear from the article) that A.A.'s macrostructure is 100% determined by the laws of physics and chemistry, the organism's structure does not simply arise on its own, but is made possible by numerous functional steps (each of which is governed by its own process), including "the fusion of two tiny motile, flagellated cells", which then "secrete a sticky substance and attach to rocks" and then begin, based assuredly on some internal signal reception, to begin the process of changing the cell wall and producing the chemical constituents that permit the formation of the "little tip that grows up toward the light". There is no evidence that these processes just happen by dint of "self-organization." - Finally, whatever may be the case with the shape of the cell wall of a single-celled organism, we need to recognize that it apparently does not apply to many, or perhaps most, of the macro structures in ourselves (example below). As a general comment, we need to be careful to distinguish between necessary and sufficient conditions. Certainly the laws of chemistry and physics influence biology, because biology is built upon and under the influence of those laws. Thus, it is always correct to observe that chemistry and physics have an influence on biological development and structure. However, that does not mean that biology (in any particular case) is simply a natural outgrowth of natural laws. One way to think about whether something is "caused" by natural law, as opposed to being simply "influenced by" or "consistent with" is to ask whether the thing in question must necessarily occur. Simple example: is there something about cartilage cells that cause them to physically arrange in the form of a nose? The answer is clearly no, because we know of other arrangements that exist. Is there anything about chemistry and physics that causes your front tooth to take the shape that it does? No. Because we can look and see that other shapes are possible. This does not mean that chemistry and physics aren't working. They are; but they didn't cause the particular structure to come about. Chance didn't either, because we see a regular, coordinated outcome across millions of examples. Thus, there must be, by necessity, some functional specified information that harnesses the laws of chemistry and physics to make this particular outcome come to pass in physical reality. There are thousands upon thousands of such machines and systems with similar information requirements. That information must reside somewhere.Eric Anderson
November 17, 2011
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Let me suggest that you at least make a small effort to learn about origin of life research, AKA "abiogenesis." A good place to start would be a "Short Outline of the Origin of Life." http://stonesnbones.blogspot.com/2008/12/origin-of-life-outline.html We do know that both peptides, and catalytic short RNA formed spontaneously, that these bind to various minerals which stabilized them, and that they were encapsulated by equally natural forming phosopholipid vesicles. We follow two lines of inquiry- geochemical studies of sedimentary rock of about the same age as the origin of life, and experimental studies of the fundamental chemistry of life as we find it today.wateron1
November 17, 2011
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Information is analogous, too. There’s pedagogical value there, but hey, this blog is a shrine to dangers of analogical thinking about information (including, notably, you specifically, Upright Biped
By the way eigenstate, information is an observable reality with physcial entailments. If you'd like to lay out each other's definitions, and see which can be substantiated from a physical perspective, I am more than happy to accept that challenge.Upright BiPed
November 17, 2011
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Hi Eric, I appreciate your response and I will address it in more detail, but in the meantime, have a look at this recent TED talk on the boundaries between life and non-life and the curious properties that emerge from very simple things.
I’m not too impressed with vague, unspecified notions about minimalist programs and self-organization.
I would urge you to read a bit of Goodwin's work on self-organisation, as I linked to before. It is surprising and unintuitive what, for example, a simple calcium gradient does in terms of generating the form of Acetabularia. I don't find the concept as vague or unspecified as you seem to - there are examples of how this works (also, to a certain extent, in Martin Hanczyc's talk linked to above).
Everything we have discovered thus far in cellular processes shows an incredible degree of carefully orchestrated and controlled processes.
Gradients of hox gene expression, in turn regulating cascading expression of other genes during ontogeny does not smack of engineering in the sense of strict control occurring at every step of the process. It is instead a rather minimal setting up of conditions from which everything else unfolds.paulmc
November 17, 2011
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Thanks, paulmc. I appreciate your thoughts on "determinism" and I don't mean to suggest that there is no environmental influence. However, I find the "spontaneous organization" ideas somewhat lacking, because they ultimately boil down to just a fancy label for a process that is governed by chance, necessity, or some combination of the two. Environmental factors may have some influence at the periphery, but they are clearly not the primary drivers of organismal development or structure. I'm more interested in the engineering aspect. What is required to build, for example, an eye, or teeth or ears, or nose? We know that this construction is contingent and is carefully controlled. For example, there is nothing about cartilage itself that causes it to self-assemble into an ear as opposed to a nose. And certainly nothing that would cause it to self-assemble in the precise location and shape. (Indeed, when the instruction set gets messed up, we occasionally see failure to develop properly.) Because these things are contingent, they cannot -- by definition -- be caused by some kind of physical or chemical law. And because they occur in a regular, controlled and organized way, they cannot be the result of pure chance. Thus far, when we have looked into the cell, we have found machines and programming and instructions, and signals, and feedbacks, and switches, and on and on. Things don't "just happen" in the cell based on vague notions. Take the bacterial flagellum. Scientists have discovered the genes that code for the various proteins. But having the various proteins in the cell does not mean that we have a flagellum. Indeed, the proteins must be organized in a highly specific sequence and location to properly produce a flagellum. This doesn't happen by simple chemical and physical attractions (although those attractions are certainly utilized in the construction and ongoing function). This doesn't happen by chance. Rather, there is a carefully orchestrated -- programmed -- process that takes place to produce the flagellum. Similarly, there are thousands upon thousands of other molecular machines, and many thousands of construction characteristics that don't happen simply by necessity or chance. We know these machines exist; we know the construction takes place; we know there must be information stored, accessed and utilized to build these machines and structures. That information doesn't come from some vague environmental influence or the laws of chemistry and physics. Rather, that information must reside somewhere in the cell. We have only scratched the surface at uncovering that information, and it would be a great marriage of ignorance and hubris to think that the information doesn't exist, based solely on the fact that we haven't found it yet. ---------- On your last point, I'm not focused on the idea that the designer(s) of life is the Christian God. Even so, to respond to your thought, I do agree that the organism has to live within an environment and must be able, within degrees, to respond to that environment. But I'm not too impressed with vague, unspecified notions about minimalist programs and self-organization. Everything we have discovered thus far in cellular processes shows an incredible degree of carefully orchestrated and controlled processes. There is every reason, from a physical and engineering standpoint, to believe that we will find the same as we continue to elucidate other machines and processes within life.Eric Anderson
November 17, 2011
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"We don’t know that “matter is all there is”, and can’t know that." Despite your attempt to couch the issue, I once again applaud you for the tacit admission that the virtual whole of biological and cosmological science is operating under a false assumption which it cannot support. And trying to rephrase it to say that "matter is all we know" simply changes one assumption for another, and therefore does nothing but highlight the irrational (non-scientific) conduct among scientists who make these claims in the name of science. "So we’re all on equal footing, but the ramifications for me aren’t even minor in terms of my belief in contrast to a theist who “knows God created the universe” Of course this only holds true if you are able to think your conclusions into being, otherwise, you live and die under the same realities as everyone else. In any case, I am happy to remind you that ID doesn't trade in questions of "eternal salvation". "On your arguments that are entirely system-internal, and predicated on material objects and dynamics, that’s great. I salute that." Then you have, at the very least, negated your argument that one must be outside our system in order to "make use" of evidence.Upright BiPed
November 17, 2011
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@Upright Biped,
So to put your position into play without contradiction, “dangling conjecture” that there is ‘something more than matter’ holds the same usefulness in obtaining knowledge as “dangling conjecture” that ‘matter is all there is’.
We don't know that "matter is all there is", and can't know that. But we can say "all we know is matter", which isn't the precise way I'd phrase that on its own, but works for the purposes of turning "matter is all there is" around. For example, in math, the Goldbach Conjecture remains an open question (equivalent to being open as to whether 'matter is all there is'), but even so, vast sets of empirical tests of the conjecture, calculating for n < 1x10^18 -- huge values of n, all of which support the idea. This matches the turnaround : "all we know is matter". All the evidence we have, and there is a LOT of it, conforms to the Goldbach's hunch. "matter is all there is" "all we know is matter", and the latter is the position that rests on a positive epistemology, with no frame jumping or anything like that needed.
Likewise, in terms of existence, someone saying that “God did it” has equal material footing as anyone saying anything else. This includes, of course, every convinced materialist alive.
Yes. And would toward that everyone could have the clarity to acknowledge that. As a materialist, it's an epistemic frustration, a question I'd very much like to know, but can't. But I've got no eternal salvation riding on any answer that gets diminised by admitting I don't know. I don't have any "oracles" I have to re-evaluate from "outside the system" I have to re-evaluate. So we're all on equal footing, but the ramifications for me aren't even minor in terms of my belief in contrast to a theist who "knows God created the universe".
I think this is an interesting admission on your part, at least to the extent that no one is fooled by it. In any case, you’ll be happy to know that the argument I make provides no claims about what may or may not exist outside our system. In fact, it is based entirely upon what is inside our system, particularly material objects and their observable dynamics.
Fooled by what? I have no problem with the epistemic parity everyone shares on this. On your arguments that are entirely system-internal, and predicated on material objects and dynamics, that's great. I salute that.eigenstate
November 16, 2011
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It okay petrushka, eigenstate accidentally posted his comment in the wrong place, I was responding to him.Upright BiPed
November 16, 2011
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"I don't know" So to put your position into play without contradiction, "dangling conjecture" that there is 'something more than matter' holds the same usefulness in obtaining knowledge as "dangling conjecture" that 'matter is all there is'. Likewise, in terms of existence, someone saying that "God did it" has equal material footing as anyone saying anything else. This includes, of course, every convinced materialist alive. I think this is an interesting admission on your part, at least to the extent that no one is fooled by it. In any case, you'll be happy to know that the argument I make provides no claims about what may or may not exist outside our system. In fact, it is based entirely upon what is inside our system, particularly material objects and their observable dynamics.Upright BiPed
November 16, 2011
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@Upright Biped,
eigenstate, if you are able to justify your conclusions without going “outside our physical system” then why, without equivocation, do you suggest that for others to justify their conclusions they would need to go “outside our physical system”?
The conclusion I have is what I began with -- "I don't know". I don't have to be outside the universe to conclude that. It's the epistemic starting point, knowledge. If another says "I don't know", I don't need any justification for that position, any more than my position needs it. If someone else says "God did it", that is to claim some knowledge. So I wonder how one would "jump outside of the system" that we are enclosed in to establish that. Or altenatively, if one accepts a claim from some other source inside the system that they have (or it has) knowledge grounded in outside-the-system experience, I wonder how they can establish the bona fides of such a frame-jumping claims.
It appears that you have used whatever you’ve seen as useful within the system to justify your position, so why would others not be afforded that same utility? Are you operating under assumption that there are nothing within the system that is of any use on the matter? If that is so, the what did you use?
There well may be a lot of resources inside the system that COULD BE of use in building knowledge about facts from outside the system. But without being able to transcend the system to investigate or test it, we can't make use of it. It may be here, but we can't use it to discern, as we are "stuck in the system". String theory, which I was just discussing with you (? or was it PaV?) is an example which may have such in-system resources that could point to "out-of-system" explanations - perhaps there was a "String Bing" that predicated the "Big Bang" as one physicist conjectured recently -- but it can't rise to anything more than that: conjecture. We can't test it, because we are physically contained by, and constrained within the system. So perhaps some string theory notion has implications that would be knowledge if we could test it regarding "out-of-system" facts. But it can't be anymore than a "perhaps", given our limitations. If you think dangling conjecture is "of any use", then I guess on your terms, there ARE items of use. But as knowledge, no, we have much fodder for conjecture, some more scientific in its origins, some less, but the key steps in knowledge building -- testing, falsification, integration of dispositive evidence, are not available to us, even in principle, so far as we can tell.eigenstate
November 16, 2011
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The simple fact is that I only have time to look at this site once in a while, and the new thread structure and the quantity of new threads means that old threads disappear very quickly. I have no idea what the old question was. I am responding to something said on this thread posted just above my response. Due to the unexpected formatting -- a post consisting entirely of nested quotes -- I don't even know who made the statement, nor do I care who made it. I am just responding to the implication that computer resources are a relevant metaphor.Petrushka
November 16, 2011
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You'll have to keep in mind that my argument has nothing to do with a computer analogy. In any case, the question you ask of me is one I have already answered. It is posted in the same thread you referenced regarding Dr Liddle. You simply have failed to respond to it.Upright BiPed
November 16, 2011
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eigenstate, if you are able to justify your conclusions without going "outside our physical system" then why, without equivocation, do you suggest that for others to justify their conclusions they would need to go "outside our physical system"? It appears that you have used whatever you've seen as useful within the system to justify your position, so why would others not be afforded that same utility? Are you operating under assumption that there are nothing within the system that is of any use on the matter? If that is so, the what did you use?Upright BiPed
November 16, 2011
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If you have every done any goofing off with 3D rendering programs, any attempt to try and “truly model and render” even a small, simple scene from real life prompts a similar kind of appreciation: the “polygon count” and “texture shaders” of reality are stupendously large and complex.
Doesn't compare with the problem of protein folding, which chemistry can do in a thousandth of a second. One of many reasons why the computing metaphor cannot be used to calculate the difficulty or improbability of phenomena in biochemistry.Petrushka
November 16, 2011
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@Upright Biped
My real issue with Eigenstate is the anthropocentric delusion that matter “computes” itself, and the bastardization of information by suggesting that everything “contains it”. Oh, I've no problem with pointing out the limits of the analogy -- and it is an analogy. The universe is not a computer. That analogy breaks down at some point, as all analogies do. It is useful conceptually, but usually I am on the other side reminding others of the limits of the analogy, as many are wont to take it where the mapping breaks down -- "Hah! Gotcha! If it's a computer than who programmed the software then? Hmmmm???" Information is analogous, too. There's pedagogical value there, but hey, this blog is a shrine to dangers of analogical thinking about information (including, notably, you specifically, Upright Biped, and I have my names right and you were the one who recently posted a longish reply to the (now departed) Dr. Liddle on information-related matters). The isomorphism with computing concepts, where it applies, is sound (decoherence, for example, mapping to the process of recomputation/re-rendering of a model which is updating in real time in a computer). But the map is not the territory.
These are very alluring and pervasive visions, one’s which lead to great uitility, but they are false and those who hold them should have the discipline to not conflate them with reality.
All over that. Back to the original idea that sparked this sub-thread though, it's difficult to locate a better set of semantic grips on the concept of "computing fitness" in nature than to invoke computing terminology. It's law-based (algorithmic), iterative (cycle-based), and resource intensive, with all of that having to run as a smooth process (computational). In evolutionary algorithms with actual computers, it's exceedingly difficult to get sufficient computing resources deployed to achieve anything more than superficial fitness tests done at scale without having to wait six months for any results. This drives an appreciation for the lavish "computing resources" (analogically speaking) of nature, which not only support real time fitness resolution, across all biological entities, but also the resolution of every other interaction in parallel with that, as well. If you have every done any goofing off with 3D rendering programs, any attempt to try and "truly model and render" even a small, simple scene from real life prompts a similar kind of appreciation: the "polygon count" and "texture shaders" of reality are stupendously large and complex. I'm curious, though. In my experience, the ditch that people fall into in my experience with computing analogies for nature is a creationist ditch; that such analogies somehow establish some kind of support for "Intelligent Developer" or something. I don't think that's your beef with the analogy. What do you see as ditch on the other side in terms of nature-as-computer analogy?
eigenstate
November 16, 2011
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@Eugene S
Excellent. Thanks. I can even see grounds for doubting if there is any semantic cargo in this question. This is as much as materialistic thought can get. Fair enough. Anyhow, we need an oracle to learn why. Who might that oracle be? I think it is the One who designed this Big Quantum Computer of nature.
Why would you think that? It's transcendentally self-defeating, that stance. Some putative oracle says "I am god, and I created you and the your entire universe". How would one test that? Why would one suppose that supposed oracle was an actual oracle in the first place? You can't get outside our system to test that claim. At all. Ever. So you are in the same epistemic position as I am -- non-knowledge, and no path to knowledge. You can say "I think it's this", there's nothing but desire for such a belief to recommend it. I certainly understand such desires, but desire doesn't help you epistemically. My reference to an oracle was a winking one; that doesn't help, and is part of the problems we have to deal with in reasoning about such question. Anyway, this is just a nuts-and-bolts example of materialist atheism demonstrating where it declines the temptation to be religious, to concoct stories where it's knowledge ends. We are not physically (!) able to jump out side our physical system, so we cannot get ANY feedback on the question of the provenance of the system IN THAT SYSTEM'S REFERENCE FRAME. So, aware of that hard limitation through reasoning about it, I acknowledge it. It's not a religiously satisfying answer. It doesn't answer the big, outer metaphysical question. It can't, so it does not. That's a feature, not a bug, as they say in the software biz.eigenstate
November 16, 2011
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Hi Eric. I think I did understand your line of thinking there. To claim this:
However, many ongoing biological processes, and virtually all of the construction processes, do not occur by simple virtue of chemical and physical interactions. Rather, they must be controlled to produce a certain result. That means a plan, initiations signals, instructions, feedback, control loops — programming.
is to assume that everything about an organism is highly deterministic. That is far from evident. A lot of 'input' comes from the environment. I am not a developmental biologist and cannot do the topic justice, but one of the main criticisms of the neoDarwinian framework came from developmental biologists who argued that genetics did little to answer these types of questions that you are asking - that in fact organisms are much more integrated systems. While the past couple decades certainly haven't borne out everything that these developmental biologists claimed, most would remain sceptical of excessively deterministic genetics. What you are proposing is an extremely high level of genetic determinism. Just as an example of what I mean, Brian Goodwin's work modelling spontaneous organisation in Acetabularia is a caution against always assuming such determinism. There's an extract from a chapter of Goodwin's work here. Again, I am not a developmental biologist; someone else could do a much better job of outlining this. Also, Goodwin was far from right about everything, and I am not holding him up as the gold standard for developmental biology. So to be clear, don't get me wrong - overall, I agree there will be much more to learn about the genome, and much of what we learn will probably be surprising, weird, counterintuitive. But I don't think we'll find millions of deterministic, but currently unknown functional instructions. As far as ID goes, I find this line of reasoning a little unusual. While I know it is meant to go unsaid here, in practice I'm sure we can agree that at least many of you ID guys personally believe that the designer was likely the Christian God, even if this is not a tenet of ID. So, why should God work in just the same way that we do? A minimal 'program' that works in concert with the environment has a sort of beautiful, simplistic elegance that I wouldn't write off, were I religious. Certainly not for the sake of a computer programming analogy.paulmc
November 15, 2011
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Scott, agreed, especially regarding our tendency to dehumanize others behind the text -- it's not the same to look into someone's face and say out loud the things we type here. I'm guilty of this as well. Thanks. mi.material.infantacy
November 15, 2011
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m.i.
I understand that when folks here refer to Christians they generally are referencing Catholics and Protestants. It’s not possible to be inclusive of all groups who self-label as Christian.
You're right. It's not practical or realistic to suggest that they do otherwise. I understand why someone shoots off. I've done it too. I'm as guilty as anybody. It's the same problem that affects the way drivers treat each other in traffic - sometimes we forget those are real people out there. It's easy to get on a soapbox, and it's all fun until someone says "Ouch!" and then it's embarrassing. I've addressed subjects in this forum in a manner that I would never, ever, do face to face. I don't mind a little more bluntness when it comes to the science aspect. It's the whole point, and it's less personal. When it comes to religion I need to hold myself to a much higher standard. There's no such thing as "winning" such a debate. It's never happened in my whole life. The best I can hope for is to drag my most cherished beliefs through the mud. So whatever I've said on more than one occasion, I apologize for undo tactlessness and pomposity.ScottAndrews2
November 15, 2011
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Hi Scott, indeed we will not agree on the Trinity, and I certainly don't expect that the debate will be resolved here. I don't necessarily mind doctrinal disagreements and discussions on occasion, and they're certain to come up on UD, as those of many faiths and denominations find something here to agree on that doesn't otherwise compromise strongly held beliefs. As I said before, I have often found your comments entertaining and insightful. And our brief debate on the Christian Darwinism thread about the Endor passage was at least amiable. I understand that when folks here refer to Christians they generally are referencing Catholics and Protestants. It's not possible to be inclusive of all groups who self-label as Christian. However I would like you to note Eocene's use of the term "Christendom" as pejorative of Catholics and Protestants. I'm well aware of the WBTS' use of that term to denote all the fallen outside of your church, so I think it's fair to presume that we disagree on what it means to be Christian. So IMO we shouldn't dissemble all-inclusiveness of the term. Neither one of us believes the other fits the definition of Christian, unless I'm mistaken about your beliefs. Things often appear just as they are, and it appears that I have little patience for Eocene's rudeness toward non-WS Christianity. I can't promise to bite my own tongue if he continues to ridicule it. I have plenty of fire in my belly for what I regard as doctrinal perversion; but I think we have already agreed, at least between the two of us, that this isn't an appropriate place for such. All that said, I too appreciate the general perspective of UD as focused on both science and evolution, and I find that in this environment I am a student, taking advantage of those better spoken and educated. I much prefer that to incessant theological disputes, as there is no lack of internet destinations suitable for those who cannot resist. I will make no solemn vow regarding my own behavior, and few apologies. I make no claims to any righteousness that's not imputed to me externally. Your level-headed and pragmatic approach to this is appreciated, and stands in contrast to the bigotry displayed by Eocene -- however it appears that both he and I would have plenty to say if the gloves were taken off. In the interest of deemphasizing our differences for the sake of others on this board, any perceived past offenses are, for my part, forgiven. I hope going forward that self-control can be exercised regarding unresolvable doctrinal disputes; otherwise I foresee a lot of back and forth about things which will likely not interest many others, and will ultimately detract from an otherwise singular environment here at UD. Best, m.i.material.infantacy
November 15, 2011
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m.i.,
The concept of The Trinity comes naturally from a plain reading of scripture. It’s not like Jesus is Michael the Archangel or something.
While I couldn't disagree more, this is why my better judgment tells me to stay away from scriptural debates on the internet. I haven't always listened to it. I will now. I'm here for the science. If someone else makes a theological statement I disagree with, I really need to bite my tongue. (It would be nice if some would be a little more considerate and refer to their specific religion rather than make blanket statements like 'Christians believe this...' But more likely I'll just have to ignore it. Oh well.) In an internet forum every house is a glass house. I've chucked my share of stones. I don't retract but I repent.ScottAndrews2
November 15, 2011
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Thanks, paulmc. My question was perhaps a bit vague, so perhaps I can clarify. By "programming" I am referring to the algorithms necessary to build and maintain the organism. In a very broad sense (applying it to us), what makes us human, as opposed to a blob of homogenous cells? There are many thousands (likely millions) of functional instructions that must be executed to create and maintain a human. We know this information must exist, and that it must exist in DNA (with perhaps some existing in the mother's egg), because that is all we start with. What causes the egg to begin to divide? What causes the cells to differentiate in the right location at the right time? And on and on. Just looking in the mirror we can see myriad pieces of informational instructions that have been carried out at some point in development. Certain cells must differentiate to form cartilage, and then they must be organized to continue in this direction until point x, then over to point y, etc., until the cartilage for a nose is formed in the right place and in the right shape. Same for the ears. Cells have to be programmed to become the various parts of teeth, at exactly the right place and time, and then as the child grows, to be replaced by a new set of larger teeth at just the right location. And on and on. There are some biological processes that take place based on the basic chemical and physical interaction between different proteins. However, many ongoing biological processes, and virtually all of the construction processes, do not occur by simple virtue of chemical and physical interactions. Rather, they must be controlled to produce a certain result. That means a plan, initiations signals, instructions, feedback, control loops -- programming. So far, we have identified some code that codes for specific proteins. We have also identified some DNA sequences that aid in protein expression (introns, LINEs and the like). We haven't even scratched the surface in understanding the rest of DNA or understanding the algorithms involved in going from a single fertilized egg to an adult human. We know these processes take place. We know they require specified information, signaling, feedback and control algorithms. And we know that much, or most, of it must be contained somewhere in DNA.Eric Anderson
November 15, 2011
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Eocene wrote:
It’s sort of like asking a member of Christendom to explain the “Trinity”. The answer usually is – “It’s a Mystery”.
The concept of The Trinity comes naturally from a plain reading of scripture. It's not like Jesus is Michael the Archangel or something. If you insist on taking classless, snarky pot shots at Christian theology, I have no lack of Watchtower ammo to return fire with. You should decide now if that's what you want going on on this board -- you mocking Catholicism, and me mocking the Watchtower. Your call.material.infantacy
November 15, 2011
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