Junk in the Trunk

| 305 Comments

Sadly I don’t have time for a full blog, but PT readers should read a caustic paper by Dan Graur et al. (Graur of chicken entrails fame), which is doing the most thorough take-down to date of the ENCODE project’s widely-advertised claim last year that 80% of the human genome is functional and that the junk DNA concept has been debunked. It’s open access, and the media is starting to pick it up: http://gbe.oxfordjournals.org/conte[…]ull.pdf+html

The major weakness is that Graur et al. do not discuss the huge variability in eukaryote genome size much, although they do cite Ryan Gregory’s Onion Test. And the tone is such that tone itself is becoming an issue. On the other hand, many of us feel that ENCODE steamrolled basic, well-known scientific facts when it shot the “80% functional” claim around the world’s media. Certainly there’s a lot to discuss!

305 Comments

The entire “controversy” is grounded in the use of imprecise language, particularly imprecise use of the term “functional”. I am on the side of those who think the ENCODE press releases greatly misused the term “functional”, but until people actually agree to use the term to mean the same thing, all dialogue is just people insulting each other for using the same word in different ways.

I think just using the term “active” instead of “functional” might have helped a great deal.

“Functional” and “junk” are both subjective terms which need to be carefully defined if conflicts about their use are to be resolved. There also needs to be some effort to be honest and consistent, though, because there will always be gray areas. If “functional” means “does something for the cell which facilitates cell survival and/or reproduction”, then mutations with negative impact, recessive alleles, and even alleles that code for proteins that work but perform a totally redundant function might not make the grade as “functional”. On the other hand, if we define “functional” as “potentially does something that impacts on cell survival and/or reproduction”, all sorts of “junk” like transposable elements meets the definition of “functional”.

Complicating it all is that it is extremely important to understand what such potentially active junk might do, whether we call what it does “functional” or not. Nothing could be more absurd than - not to imply anyone would do this - inhibiting or disparaging study of the role of genome elements validly considered junk, in things like causing neoplasms or infection, susceptibility, by affecting protein or RNA expression, or chromosome stability, through recombination, transposition, etc, out of fear that creationists might claim that such study means that something is “functional”.

I will illustrate what I am talking about with the example of TURF13.

As readers here may recall, the TURF13 story goes approximately like this (feedback welcome if corrections or elaborations are relevant). Some loci in the genome of a strain of maize recombined to come together in one or more events. Prior to the recombination these loci represented functionless junk by reasonable standards. Now they are a single locus which codes for an expressed protein. But here’s the real catch - so far, all the new protein has been shown to do is to make the maize strains that carry it susceptible to a particular fungal infection. It may have some sort of beneficial activity as well, but that hasn’t been detected, to the best of my knowledge.

Is the TURF13 gene functional? It codes for a protein. Were the loci that recombined to create it functional? Almost certainly not, but they were “active”.

harold Wrote:

The entire “controversy” is grounded in the use of imprecise language, particularly imprecise use of the term “functional”.

In fact, as you know, the entire anti-evolution movement is “grounded in the use of imprecise language.” Including quote mining those who have no problem with evolution to pretend that they do.

Including quote mining those who have no problem with evolution to pretend that they do.

Sure, but they just go for evolution because they hate God.*

Oh, and have the absurd notion that science should be about something.

Silly stuff like that.

Glen Davidson

*Easily proven by the great conviction of anti-evos that they must hate God

Nick,

Bozo Joe is once again infesting these threads using a different name. As you know, he was permanently banned for threatening violence against anyone who disagreed with his insane ideas. Pleas dump all of his posts to the bathroom wall immediately until he can once again be banned. If you don’t do this, this thread will become filled with the most vile and insane nonsense imaginable. Joe is psychotic and completely irrational, he simply cannot handle the truth. Do him a favor and put him out of our misery.

Is the TURF13 gene functional? It codes for a protein. Were the loci that recombined to create it functional? Almost certainly not, but they were “active”.

TURF13 causes cytoplasmic male sterility, which actually can be “functional” at least in the way that other classic “selfish genes” are functional, i.e. they propagate themselves in the population. I think from the perspective of the organism a purely selfish gene may not be considered functional, although in the case of Turf13 other things may be going on as well.

http://en.wikipedia.org/wiki/Cytopl[…]le_sterility

For added fun & excitement, see the twitter discussion: https://twitter.com/DanGraur

DS said:

Nick,

Bozo Joe is once again infesting these threads using a different name. As you know, he was permanently banned for threatening violence against anyone who disagreed with his insane ideas. Pleas dump all of his posts to the bathroom wall immediately until he can once again be banned. If you don’t do this, this thread will become filled with the most vile and insane nonsense imaginable. Joe is psychotic and completely irrational, he simply cannot handle the truth. Do him a favor and put him out of our misery.

Point out which ones so I can click them, I haven’t been following comments lately…

Anything by a Masked Panda (1686), such as the one directly prior to my post. Joe has been using that name for a few days now. And he will undoubtedly change names once again when he is banned. He is absolutely obsessed over the idea of junk DNA. He is not emotionally capable of letting the discussion continue without trying to interrupt it.

harold said:

The entire “controversy” is grounded in the use of imprecise language, particularly imprecise use of the term “functional”. I am on the side of those who think the ENCODE press releases greatly misused the term “functional”, but until people actually agree to use the term to mean the same thing, all dialogue is just people insulting each other for using the same word in different ways.

I think just using the term “active” instead of “functional” might have helped a great deal.

“Functional” and “junk” are both subjective terms which need to be carefully defined if conflicts about their use are to be resolved. There also needs to be some effort to be honest and consistent, though, because there will always be gray areas. If “functional” means “does something for the cell which facilitates cell survival and/or reproduction”, then mutations with negative impact, recessive alleles, and even alleles that code for proteins that work but perform a totally redundant function might not make the grade as “functional”. On the other hand, if we define “functional” as “potentially does something that impacts on cell survival and/or reproduction”, all sorts of “junk” like transposable elements meets the definition of “functional”.

Complicating it all is that it is extremely important to understand what such potentially active junk might do, whether we call what it does “functional” or not. Nothing could be more absurd than - not to imply anyone would do this - inhibiting or disparaging study of the role of genome elements validly considered junk, in things like causing neoplasms or infection, susceptibility, by affecting protein or RNA expression, or chromosome stability, through recombination, transposition, etc, out of fear that creationists might claim that such study means that something is “functional”.

I will illustrate what I am talking about with the example of TURF13.

As readers here may recall, the TURF13 story goes approximately like this (feedback welcome if corrections or elaborations are relevant). Some loci in the genome of a strain of maize recombined to come together in one or more events. Prior to the recombination these loci represented functionless junk by reasonable standards. Now they are a single locus which codes for an expressed protein. But here’s the real catch - so far, all the new protein has been shown to do is to make the maize strains that carry it susceptible to a particular fungal infection. It may have some sort of beneficial activity as well, but that hasn’t been detected, to the best of my knowledge.

Is the TURF13 gene functional? It codes for a protein. Were the loci that recombined to create it functional? Almost certainly not, but they were “active”.

Good point. Sequence conservation is a good indicator of functional constraint. SInce mutations are random, all sequences will eventually mutate and natural selection will act to weed out the deleterious changes. Therefore, functional constraint will lead to a very precise pattern of sequence divergence and conservation in constrained and unconstrained sequences. However, some nucleotides have a “function” even if the nucleotide sequence is not constrained. So the exact definition of “function” is critical is this is the test to be applied. FOr example, the exact number of nucleotides between the promotor and the site of initiation of transcription is critical to proper gene expression, but only a few of the nucleotides in the sequence are conserved.

That having been said, there is a large proportion of the human genome that has no known “function”. The sequence could be anything, or it could be missing completely with no effect whatsoever on phenotype. This is the result of the evolutionary process and the limitations of naturals selection with respect to these characters. To pretend that the genome is “designed” or “efficient” or the product of anything other than these natural forces is contrary to all of the evidence. You can believe it is you want and you can say it as often as you like, but that doesn’t make it true.

DS said:

harold said:

The entire “controversy” is grounded in the use of imprecise language, particularly imprecise use of the term “functional”. I am on the side of those who think the ENCODE press releases greatly misused the term “functional”, but until people actually agree to use the term to mean the same thing, all dialogue is just people insulting each other for using the same word in different ways.

I think just using the term “active” instead of “functional” might have helped a great deal.

“Functional” and “junk” are both subjective terms which need to be carefully defined if conflicts about their use are to be resolved. There also needs to be some effort to be honest and consistent, though, because there will always be gray areas. If “functional” means “does something for the cell which facilitates cell survival and/or reproduction”, then mutations with negative impact, recessive alleles, and even alleles that code for proteins that work but perform a totally redundant function might not make the grade as “functional”. On the other hand, if we define “functional” as “potentially does something that impacts on cell survival and/or reproduction”, all sorts of “junk” like transposable elements meets the definition of “functional”.

Complicating it all is that it is extremely important to understand what such potentially active junk might do, whether we call what it does “functional” or not. Nothing could be more absurd than - not to imply anyone would do this - inhibiting or disparaging study of the role of genome elements validly considered junk, in things like causing neoplasms or infection, susceptibility, by affecting protein or RNA expression, or chromosome stability, through recombination, transposition, etc, out of fear that creationists might claim that such study means that something is “functional”.

I will illustrate what I am talking about with the example of TURF13.

As readers here may recall, the TURF13 story goes approximately like this (feedback welcome if corrections or elaborations are relevant). Some loci in the genome of a strain of maize recombined to come together in one or more events. Prior to the recombination these loci represented functionless junk by reasonable standards. Now they are a single locus which codes for an expressed protein. But here’s the real catch - so far, all the new protein has been shown to do is to make the maize strains that carry it susceptible to a particular fungal infection. It may have some sort of beneficial activity as well, but that hasn’t been detected, to the best of my knowledge.

Is the TURF13 gene functional? It codes for a protein. Were the loci that recombined to create it functional? Almost certainly not, but they were “active”.

Good point. Sequence conservation is a good indicator of functional constraint. SInce mutations are random, all sequences will eventually mutate and natural selection will act to weed out the deleterious changes. Therefore, functional constraint will lead to a very precise pattern of sequence divergence and conservation in constrained and unconstrained sequences. However, some nucleotides have a “function” even if the nucleotide sequence is not constrained. So the exact definition of “function” is critical is this is the test to be applied. FOr example, the exact number of nucleotides between the promotor and the site of initiation of transcription is critical to proper gene expression, but only a few of the nucleotides in the sequence are conserved.

That having been said, there is a large proportion of the human genome that has no known “function”. The sequence could be anything, or it could be missing completely with no effect whatsoever on phenotype. This is the result of the evolutionary process and the limitations of naturals selection with respect to these characters. To pretend that the genome is “designed” or “efficient” or the product of anything other than these natural forces is contrary to all of the evidence. You can believe it is you want and you can say it as often as you like, but that doesn’t make it true.

I completely agree with this.

It is interesting and poorly explained that most (although not all) eukaryotic genomes do carry vast amounts of DNA that is neither coding nor regulatory, much of which is shown to be completely redundant - transgenic mice with massive deletions of junk DNA appear normal, for example, if I recall correctly (I can’t recall if they can breed with wild type mice and would appreciate updating if anyone does know - a brief search wasn’t successful). At least some of this DNA is potentially harmful. Much of it experiences no sequence specific selection (which makes it very useful for different types of kinship analysis). On the other hand, having it certainly isn’t selected against, either, in most eukaryotic lineages.

One extreme definition of “functional” would be a very strict one requiring association with a gene coding for a working protein or RNA, another extreme definition would be to call anything that has any activity functional, which would amount to all of the genome if we call being replicated a form of activity, and much of it even if we require transcription for “activity”, because there is low level transcription of junk DNA that isn’t even associated with regulatory elements. Much of the firestorm really is semantic, and driven by unspoken concern about potential creationist distortions.

In my view, we should never worry too much ahead of time whether creationists might distort - they will, no matter what science says.

I was going to point out that Joe’s arguments in this thread border on contradicting his arguments in prior threads.

Previously, all mutations were negative, and thus, by definition, all life would have to be deteriorating from some original baseline defined by Joe as ideal.

Now, suddenly, contemporary junk DNA is wonderful and perfectly functional, despite the fact that it contains numerous polymorphisms.

Well the definition of “functional” cannot be that it could one day take on some function. We know that any random sequence can mutate into something “functional”. All DNA represents the raw material on which natural selection can act. But then again, creationists can’t use this definition, not without admitting that random mutaion and natural selection can produce new information, new genes, new functions and new structures. And that was the reason for all this bluff and bluster about “junk DNA” in the first place. So for once it’s heads evolution wins and tails creationism fails.

DS said:

Well the definition of “functional” cannot be that it could one day take on some function. We know that any random sequence can mutate into something “functional”. All DNA represents the raw material on which natural selection can act. But then again, creationists can’t use this definition, not without admitting that random mutaion and natural selection can produce new information, new genes, new functions and new structures. And that was the reason for all this bluff and bluster about “junk DNA” in the first place. So for once it’s heads evolution wins and tails creationism fails.

Nothing in the above can in any way be supported.

Nick, see the above post for Bozo Joe.

I called it. This guy is as predictable as the next number in the Fibonacci series.

I think you guys should all read Graur et al., which as Nick mentions is open-access. Everything anyone has said so far was addressed in that paper, and pretty well, I think.

Looks like I don’t have sufficient admin status for doing bannings, so try to ignore him, I’ll BW as able.

Nick Matzke said:

Looks like I don’t have sufficient admin status for doing bannings, so try to ignore him, I’ll BW as able.

Thanks Nick. I appreciate your efforts.

Hear, hear.

John Harshman said:

I think you guys should all read Graur et al., which as Nick mentions is open-access. Everything anyone has said so far was addressed in that paper, and pretty well, I think.

Good point. The paper lists three types of sequences that are transcribed but have no function. These include pseudogenes, introns and mobile elements such as SINES and LINES. These three types of sequences comprise a significant proportion of the human gnome. They are counted as “functional” by the ENCODE project, even though they serve no function. So ENCODE is just plain wrong and one must conclude that they have some political or religious agenda rather than the service of science.

From page 31:

“Third, numerous researchers use teleological reasoning according to which the function of a stretch of DNA lies in its future potential. Such researchers (e.g., Makalowski 2003; Wen et al. 2012) use the term “junk DNA” to denote a piece of DNA that can never, under any evolutionary circumstance, be useful. Since any piece of DNA may become functional, many are eager to get rid of the term “junk DNA” altogether. This type of reasoning is false. Of course, pieces of junk DNA may be coopted into function, but that does not mean that they presently are functional.”

Man these guys are smart.

From page 32:

“It has been pointed to us that junk DNA, garbage DNA, and functional DNA may not add up to 100% because some parts of the genome may be functional but not under constraint with respect to nucleotide composition. We tentatively call such genomic segments “indifferent DNA.” Indifferent DNA refers to DNA sites that are functional, but show no evidence of selection against point mutations. Deletion of these sites, however, is deleterious, and is subject to purifying selection. Examples of indifferent DNA are spacers and flanking elements whose presence is required but whose sequence is not important. Another such case is the third position of four-fold redundant codons, which needs to be present to avoid a downstream frameshift.”

Now where have I heard that before?

So ENCODE is just plain wrong and one must conclude that they have some political or religious agenda rather than the service of science.

A rare instance of mild disagreement (in the context of overall agreement with all of your other statements). I may be proven wrong by evidence that ENCODE had such an agenda. But I favor a far more innocent explanation. (In this narrow, specific case. It is a good general rule that someone saying something that they “should know better than” is often a sign of a hidden agenda at work.)

I’m going to say that it’s far more likely to have been a case of two things -

1) A legitimate desire not to miss anything that could be “functional”, using a broad definition. That’s perfectly reasonable. “We made note of every part of the genome that is transcribed at any significant rate, in case that information is useful for any reason in the future”. Perfectly reasonable. “We had to err on the side of either being too inclusive or being too stringent, and for this type of study, it made more sense to err on the inclusive side”. Not a problem. Just say that you erred on the side of inclusion.

2) Obnoxious but not deliberately dishonest mis-communication.

The correct description of the work is - “Using an extremely loose definition of ‘function’, ENCODE generated an enormous database of DNA sequences; however, because this was a broad fishing expedition, most individual entries need to be viewed with caution. Our goal was to try not to miss anything.”

They overstated the overall significance of their results to the general public. Reprehensible but common. No hidden agenda is necessarily present.

(To repeat something we all agree with - as I have noted repeatedly, a lack of junk DNA would not favor creationism. That’s like saying that one less bloody fingerprint would make Charles Manson innocent. Just because junk DNA is an insurmountable problem for creationists does not mean that its absence would strengthen the case for creationism. It’s just one of many insurmountable problems.)

Or perhaps they just wanted their results to be controversial and generate some publicity. Unfortunately, it seems to have backfired.

In any event, the rebuttal paper seems to agree with me. So I conclude that they got it right. :)

Or perhaps they just wanted their results to be controversial and generate some publicity. Unfortunately, it seems to have backfired.

That sounds about right.

I enjoyed the suggested parallels between the genome and “bloatware”, which generally refers to humongous software projects written by many different people over an extended period of time, all of which is ideosyncratically documented (if at all). During this period, features are dropped or de-emphasized, debugged, patched, worked around, extended, and otherwise mangled.

Graur’s programming contacts divided such computer code into categories - functional and useful, dead, and useless. The functional useful part is obvious. But dead (that is, unreachable via any path) code nonetheless sometimes ends up performing the equivalent of spacing or alignment utility (masking bugs elsewhere).

Useless code, now, is fascinating and seems very like much of what ENCODE identified. Useless code is reached during execution, and performs functions - it can produce values, modify data structures or files, etc. What makes it useless is that nothing elsewhere in the system uses or even notices these functions. It can also be essential for spacing and alignment (like dead code), for consuming bus cycles that can mask potential race conditions, for introducing delays that let IO operations complete, and so on (and on and on. BTDT.)

I think it would be a mistake to dismiss useless code as non-functional. Perhaps like a pseudogene, it might someday do something useful again. For now, it’s just noise but it DOES execute, it DOES perform functions, it’s expensive to try to identify it and weed it out, so over time it just keeps growing.

Actually, as the paper points out, only about ten percent of pseudogenes are transcribed. So most are not “executed” at all and none perform any “function”. Not a very good design really.

IMHO some of you guys are too lenient towards the ENCODE guys especially towards Ewan Birney. I don’t know if re-defining “funcrional” was just a cheap trick or if he really wasn’t aware of 40 years of population genetics, molecular and evolutionary biology. I tend to think the later is true because he seemingly didn’t grasp the C-value paradox.

Nick Matzke said:

For added fun & excitement, see the twitter discussion: https://twitter.com/DanGraur

Indeed a source of good entertainment.

Watching the Discovery Institute and UD cluster with glee around the ENCODE project’s claims is like watching flies cluster. You know something is rotten already.

stevaroni said:

prongs said:

Einstein’s relativity is not needed when you use this Theory.

Apparently, true conservatives don’t like relativity just as much as they don’t like evolution.

Earlier today, while I was looking for examples of how 2LOT is described, I made the bad decision to peek at Conservapedia, to see what science haters would make out of thermodynamics.

But it’s OK, conservatives love the 2nd law. Because…

The Second Law of Thermodynamics is the result of the fundamental uncertainty in nature, manifest in quantum mechanics, which is overcome only by intelligent intervention.

The Second Law of Thermodynamics disproves the atheistic Theory of Evolution and Theory of Relativity, both of which deny a fundamental uncertainty to the physical world that leads to increasing disorder.

(http://www.conservapedia.com/Second[…]ermodynamics)

What’s wrong with relativity, you ask?

Relativity has been met with much resistance in the scientific world. To date, a Nobel Prize has never been awarded for Relativity.

Louis Essen, the man credited with determining the speed of light, wrote many fiery papers against it such as The Special Theory of Relativity: A Critical Analysis.

Relativity is in conflict with quantum mechanics,[8] and although theories like string theory and quantum field theory have attempted to unify relativity and quantum mechanics, neither has been entirely successful or proven.

(http://www.conservapedia.com/Theory_of_Relativity)

Instructively, it goes on at great lengths to demonstrate that Eddington’s experiments are rigged, hyper-accurate clocks do not demonstrate time dilation when moved, and cannot explain (the “arrow of time”), specifically allowing for theoretical time travel (e.g., wormholes) and different rates of passage of time based on velocity and acceleration.

Sadly, Conservipedia notes that relativity has a stranglehold on the teaching of physics

For example, Democratic President Barack Obama helped publish an article by liberal law professor Laurence Tribe to apply the relativistic concept of “curvature of space” to promote a broad legal right to abortion. (it’s quite an interesting footnote - ED)

The Theory of Relativity enjoys a disproportionate share of federal funding of physics research today.

But.. there’s hope…

Despite censorship of dissent about relativity, evidence contrary to the theory is discussed outside of liberal universities.

Stevaroni,

You are indeed correct. I often go to Conservapedia for a good belly laugh.

My very most favorite exposition about the 2nd Law is here:

http://www.theonion.com/articles/ch[…]-law-of,281/

If you already know it I apologize, but it is so good it bears reading again and again. It’s that good.

Malcolm said:

So, SteveP has no understanding of thermodynamics or biochemistry.

I wonder what he thinks happens when a protein in a cell gets damaged.

It is as if he thinks that the cell is doomed. That would make photosynethsis a little tricky.

No, Steve P thinks that the Intelligent Designer uses magic to make everything better. And we have to believe that’s the case because he’s too busy making a fortune in fabrics to check.

Mike Elzinga said:

prongs said:

Mike Elzinga, do you have a good source for the criteria used to judge electromagnetic signals from space? Too periodic or too random a signal doesn’t make for a good “Hello Universe” message. Unmodulated signals are pretty much useless as identifiers of ‘intelligence’. Modulated signals with a combination of some periodicity and pseudo-randomness seem to me to be the best candidates. Got any useful links?

Paul Davies has a book in paperback entitled The Eerie Silence, copyright in 2010.

It gives a pretty good overview of, and a critical look at, SETI and the really difficult problems with detecting intelligence; especially the problem called the “anthropocentric trap” in which we as an intelligent species keep looking for a species that will look, think, and behave like us.

When you realize that even other intelligent species on this planet don’t perceive and think like us, you have to ask yourself, “What do we look for?”

ID/creationists are babes lost in the thickets of their own making. They think simplistic “Dumbski filters” and amateur (pre high school) probability calculations are going to do it for them. However, since they don’t even understand the basics of science, what phenomena do they think they can sort on?

Is some kind of “intelligence” trying to send us a message using Saturn?. ID/creationists don’t know what they are seeing in this image. If they try to get off the hook by asserting it is natural, then they are going to have to explain where the cutoff to “natural” occurs in the physical world.

They don’t have a clue about where such a cutoff occurs in the chain of complexity in condensed matter. To ID/creationists, the behaviors of atoms and molecules are “natural” until it comes to things like proteins or the origin of life. Then, all of a sudden, atoms and molecules need “intelligence guidance” to do what they do; but they never explain just where the physics stops and “information” starts pushing atoms and molecules around.

But, according to ID/creationist “probability calculations” atoms and molecules are inert; you throw them up in the air and calculate the probability that they will come down in some specified pattern and conclude that evolution and the origing of life can’t happen.

I often wonder if ID/creationists can tie their shoes.

Mike,

I haven’t had the opportunity to read the book yet. I have found scant explanations on-line. Only Wikipedia has given the details I seek for the carrier, modulation, and message. Their discussion of the Arecibo Message gives the carrier, a frequency of ionized hydrogen I believe, the modulation, 10 Hz FSK which I suppose is carrier +/- 5 Hz with bit lengths of 100ms, and the message, a clever concoction of information for the aliens. Let’s hope the aliens perceive time like we do, have recording instruments like we do, and use radio frequency photons like we do.

What if they use light-frequency photons, or neutrinos, or gravitons, or circular polarization, or octal quantization? I don’t know what SETI is looking for, but I’ve seen nothing to suggest that they, or we, have any idea what to expect except messages from a ‘civilization’ just like us.

So to answer phhht’s question, “How do you detect intelligent design?”, the answer is, “Look for something just like human design, but comes from outer space.”

If that’s all they’ve got, then SETI is pathetic.

Their greatest contribution may be the understanding that the only design we can recognize is human design.

There is NO design we can be certain of, other than human design.

Are you looking for extraterrestrial design? Then look for human designs.

Are you looking for divine designs or supernatural designs? Then look for human designs.

Are you looking for natural designs? Well, we can point to many of those, but we know they have perfectly good natural explanations.

Man created God in his own image. Finding intelligent (divine) designs in Nature is just the reflection of our own intelligence.

prongs said:

So to answer phhht’s question, “How do you detect intelligent design?”, the answer is, “Look for something just like human design, but comes from outer space.”

If that’s all they’ve got, then SETI is pathetic.

Their greatest contribution may be the understanding that the only design we can recognize is human design.

There is NO design we can be certain of, other than human design.

Are you looking for extraterrestrial design? Then look for human designs.

Are you looking for divine designs or supernatural designs? Then look for human designs.

Are you looking for natural designs? Well, we can point to many of those, but we know they have perfectly good natural explanations.

Man created God in his own image. Finding intelligent (divine) designs in Nature is just the reflection of our own intelligence.

When it comes right down to it, looking for signals we can understand has the built-in implication that the beings transmitting those signals perceive the universe much the way we do, and build transmitting equipment much the way we would.

So the only thing we can think to look for will be things we can think of to send.

If what we understand of evolution is true, the odds are pretty small that beings like us will have emerged on other planets that are nearby.

And if such beings did in fact evolve in the broader reaches of out galaxy, or in other galaxies, the probability of their signal intercepting our planet when we just happened to be listening is much smaller.

On the other hand, if we never search, then the probability that we will intercept a signal is exactly zero.

Compared to wars and the wasted “research” that goes on in the bowels of places like the Pentagon, the cost is miniscule.

Mike,

Yes, I think that’s a good summary.

I do like Carl Sagan’s depiction of the alien message in the movie Contact. On the simplest level it has a pattern perceptible at a human scale of listening that repeats a sequence of prime numbers. Further inspection reveals human television transmissions embedded more deeply. This tells them that the aliens recognize us and acknowledge us. Even more deeply are embedded the designs to construct a communications device.

Now this is very clever. What it really represents is what we humans might do if we received television signals from another planet orbiting a distant (but not too far) star.

It is precisely the way we might respond to them. In this movie Sagan created the aliens in our own image. That’s because we have no other image with which to create aliens or gods.

I remember an article Sagan wrote for Parade magazine, the one that comes with your Sunday paper. In it he wrote that in medieval times people feared demons coming at night, paralyzing them, and transporting them out of their beds for unspeakable abominations. Now that we have ‘aliens’, people imagine them coming in the middle of the night, paralyzing them, and transporting them out of their beds to the alien ships for unspeakable abominations. Might there be a connection here?

You’ve been around long enough to recognize there are precious few creationist arguments, and none of them are really new.

Thanks for your comments.

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