Let’s Talk Junk (Again).

| 80 Comments

Back in the middle of last month, I had a few things to say about Casey Luskin (DI flak) and his understanding of so-called junk DNA. It’s now the middle of the month again, and Casey is again talking a lot - and understanding very little - about “junk” DNA. Larry Moran has a post up where he tries to educate Casey about the fact that a hell of a lot of DNA is still, at least as far as we know, junk. I’m going to take a look at something a little bit different - one of the methods scientists use to identify areas of “junk” DNA that have important functions. It’s a pretty cool way of doing things, but it’s not one that Casey likes to talk about - because it’s really one of the finest examples of how our understanding of Darwinian evolution has lead to new discoveries about living things.

Read more (at The Questionable Authority):

80 Comments

The reference to monthly cycles suggests a hormonal component to this discussion of “junk DNA”. Is it that everyone is a little tired of the “blondeness” of Casey’s arguments or is there something new here? Perhaps everyone is just a little cranky this Monday?

Since comparative genomics is no easy task I suspect everyone is a little cranky.

Delta Pi Gamma (Scientia et Fermentum)

Casey’s arguments are bogus.

Therefore there is no God.

Isn’t that what this is all about?

Basement Activist or Blair or whoever you are. Why don’t you troll somewhere else. You have not said anything close to intelligent and most of us are aware that you are posting under multiple names. At the very least, choose a name and stick with it, out of common courtesy or just out of the fear that you may be banned from posting.

There may be a God. There may not.

Either way, Casey’s arguments ARE bogus. They’re not even arguments, they’re what we laymen call “bull$#!+”.

Fighting over the philisophical problems invovled in analyzing DNA is fun to watch from the sidelines. I am not a biology major (nor did I stay at a Holiday Inn Express last night) but I’m LUCID enough to know the ID crowd are lunatic Christians (some of you who are fighting the good fight against these loonies might want to check their Christian Reconstructionist credentials).

On the other hand, and this is obviously a lay opinion…I think the ‘junk’ is just stuff scientists haven’t worked out a purpose for. Of course it’s also possible that nature worked out a way for extraneous DNA to be acquired and really have no knowable greater purpose.

In the end, whatever is discovered will be the work of true biology and not the Scooby Doo Dinosaur Team (IDiots).

Enjoy.

How is this for a ID prediction. When scientists “begin” to decipher the remaining 99% of the human genome, not deciphered by ENCODE so far, they will find an increasing amount of interwoven complexity that astounds them. The interwoven complexity will be so thorough that it will clearly demonstrate that the genome is clearly a integrated whole thus ruling out evolution.

Given that: (a) “interwoven complexity” is an entirely undefined term and unmeasurable quantity; (b) “interwoven complexity” is apparently something that has both an “amount” and can be “so thorough”; (c) it’s unclear exactly why the genome isn’t already considered to be “a [sic] integrated whole,” and; (d) no explanation is given for why discovering that the “so thorough” “amount” of “interwoven complexity” that finally reveals the genome to be “a [sic] integrated whole” would “rul[e] out evolution,”

that sounds exactly like an Intelligent Design prediction. Well done.

Re “not the Scooby Doo Dinosaur Team”

But but… Scooby Doo is smart for one of his kind. ;)

Henry

Re “that sounds exactly like an Intelligent Design prediction. Well done.”

Also a prediction of a theory has to logically follow from the premise of that theory.

Add that a bioengineer could either (1) exclude all unused stuff or (2) include some for whatever reason, the basic premise doesn’t imply anything either way regarding the question of unused DNA segments. So that so-called prediction follows (if it does) from secondary, unstated premise(s).

Henry

Bond, Blair Bond Wrote:

When scientists “begin” to decipher the remaining 99% of the human genome, not deciphered by ENCODE so far,

Here is the prediction of TR Gregory, “an evolutionary biologist specializing in genome size evolution”:

TR Gregory Wrote:

What is new about this [ENCODE] study is the fine focus being applied to the search for functional elements. By way of analogy, this study is like a group of 35 treasure hunters with metal detectors and sifters combing the same 35m of a 3.5km long beach. […] But, again, this particular study is based on only 1% of the genome and one should exercise caution in extrapolating it to the entire human genome. […] 5% of the genome sequence is conserved across mammals, and for about 60% of this (i.e., 3% of the genome) there is additional evidence of function. This includes the protein-coding exons as well as regulatory elements and other functional sequences. So, at this stage, we have increasingly convincing evidence of function for about 3% of the genome, with another 2% likely to fall into this category as it becomes more thoroughly characterized. […] We are also left with the question of why a pufferfish would require only 10% as much non-coding DNA as a human whereas an average salamander needs 10 times more than we do. The well known patterns of genome size diversity make it difficult to explain the presence of all non-coding DNA in functional terms, even as there is growing evidence that a significant portion of non-coding DNA is indeed functionally important.

So, based on 1 % of the genome in 23 mammals, the ENCODE project implies by way of evolutionary theory that between 3 and 5 % of the typical genome is functional. This is consistent with genomes such as the pufferfish and earlier rough predictions that at most 20 % of the genome is functional. (IIRC, Gregory again.)

Some suggested other (non-preserved sequence) functionality for genome is that its size correlates with cell size, so it may have a quantitative “filler” role in some species tissues.

Hmm. So by way of the contrafactual ID prediction above, it is urgent to figure out what should be lettered on ID’s gravestone.

What about:

Once a stupidity, always an IDiocy.

Right. Except that it should go:

Once an IDiocy. Always a stupidity.

Not that we can get enough of suggestions here - I can’t wait to see it realized.

Bond, James Bond– Don’t listen to them, sweetie. You did make an ID prediction, and that’s a good thing. Bravo. The only thing is, in science, predictions not only have to be made, they have to be tested. So far, your prediction is untested, so all it merits is a shrug. If your theory is tested and shot down, are you going to acknowledge you were wrong? Or are you going to pretend you meant something else and flip on to another untested theory, which IF it were proven true would shoot down evolution.… And so on. I seriously doubt that theism is what really bothers most of us about ID. The thing that’s so irritating is your endless refusal to test a hypothesis–any hypothesis– and reject it if it doesn’t fit the data. In other words, your refusal to do science.

Thanks for your civility hoary puccoon. This is strange for you to accuse ID of failing to make concrete predictions. Like for instance, Behe always predicted IC (irreducible complexity) and IC has not been refuted with anything more than preposterous “just so” stories from naturalists, thus scientifically the IC prediction stands. What’s even more problematic for naturalists is that naturalists will say that most of the DNA is now junk. Yet when it is found in the future that most all of the DNA does indeed have function and is indeed an integrated whole the naturalists will severely modify their theory so as to reflect this. So the truth is that naturalists fail to make concrete predictions. Iam confident I will not be found wrong in the complexity prediction because of the prediction track record so far,

1. Materialism did not predict the big bang. Yet Theism always said the universe was created.

2. Materialism did not predict a sub-atomic (quantum) world that blatantly defies our concepts of time and space. Yet Theism always said the universe is the craftsmanship of God who is not limited by time or space.

3. Materialism did not predict the fact that time, as we understand it, comes to a complete stop at the speed of light, as revealed by Einstein’s special theory of relativity. Yet Theism always said that God exists in a timeless eternity. 4. Materialism did not predict the stunning precision for the underlying universal constants for the universe, found in the Anthropic Principle. Yet Theism always said God laid the foundation of the universe, so the stunning unchanging clockwork precision found for the various universal constants is not at all unexpected for Theism. 5 Materialism predicted that complex life in this universe should be fairly common, Yet statistical analysis of the many required parameters that enable complex life to be possible on earth reveals that the earth is extremely unique in its ability to support life in this universe. Theism would have expected the earth to be extremely unique in this universe. 6. Materialism did not predict the fact that the DNA code is, according to Bill Gates, far, far more advanced than any computer code ever written by man. Yet Theism would have naturally expected this level of complexity in the DNA code. 7. Materialism presumed a extremely beneficial and flexible mutation rate for DNA, which is not the case at all. Yet Theism would have naturally presumed such a high if not, what most likely is, complete negative mutation rate to an organism’s DNA. 8. Materialism presumed a very simple first life form. Yet the simplest life ever found on Earth is, according to Geneticist Michael Denton PhD., far more complex than any machine man has made through concerted effort. Yet Theism would have naturally expected this complexity. 9. Materialism predicted that it took a very long time for life to develop on earth, Yet we find evidence for photo-synthetic life in the oldest sedimentary rocks ever found on earth (Sarah Simpson, Scientific American, 2003). Theism would have expected this sudden appearance of life on earth. 10. Materialism predicted the gradual unfolding of life to be self-evident in the fossil record. The Cambrian Explosion, by itself, destroys this myth. Yet Theism would have expected such sudden appearance of the many different and completely unique fossils in the Cambrian explosion.

11. Materialism predicted that there should be numerous transitional fossils found in the fossil record. Yet fossils are characterized by sudden appearance in the fossil record and stability as long as they are found in the fossil record. There is not one example of transition between major species out of millions of collected fossils. Theism would have expected fossils to suddenly appear in the fossil record with no evidence of transition to dramatically new forms.

I am somewhat confused on part of the evolution process. Please, claify this for me.

As I understand it, random mutations account for part of our evolution. Did these randomly mutated creatures have to find other similarly randomly mutated creatures to mate with in order to carry on the mutated beneficial gene; or were these mutations of the kind that does not require a like-mutation to procreate?

Let me add that mutations that need another like-mutation to procreate have never been proven by any type of inbreeding, have they? Inbreeding has always proven to be very unbeneficial to the survival of the species.

Which leads to my last question . .

I have been reading for the last few years now, that there is a consensus among the majority, that humans have been genetically traced to a two human ancestory: A genetic “Adam and Eve”.

If this is true, how is it possible that these two humans, and their immediate offspring (who had to mate with their parent or siblings at first) came to evolve at all since what inbreeding shows us, the small gene pool would have produced inbreds that may as well have been lead fed, as far as beneficial mutations of any type go.

I welcome your comments, because I don’t understand, and I really want to.

Thank you.

Bond, James Bond, “Predict”

Inigo Montoya: You keep using that word. I do not think it means what you think it means.

On the other hand, and this is obviously a lay opinion…I think the ‘junk’ is just stuff scientists haven’t worked out a purpose for.

Whose purpose? Purposes belong to planners; it is semantically nonsensical to talk about purposes as if they were intrinsic to objects.

Of course it’s also possible that nature worked out a way for extraneous DNA to be acquired and really have no knowable greater purpose.

Do you think nature has a frontal lobe?

Nature is what is and what happens. It doesn’t have purposes, it doesn’t work out ways. You might as well talk about whether mountains acquire erosion in order to let trees grow on them.

Casey’s arguments are bogus.

Therefore there is no God.

Isn’t that what this is all about?

It’s hard to fathom the lack of intellectual prowess and logical acumen that might lead one to think that “this is all about” an absurd non sequitur, although one can successfully predict that ID will continue to attract such people.

Pam:

Those are a reasonable set of questions, based around some very common misconceptions about the way evolution works. I’m running out the door to catch a flight right now, and won’t be back home until late this evening, but I’ll try to answer them then. When I do, it won’t be in this thread. The response is going to be long enough that I’ll put it up as a new post on the front page. I’ll send you an email when I do.

Pam Singer: For a more complete explanation, be sure to go to talkorigins.org and search on your questions. for instance, there does not exist any sort of scientific concensus such

that humans have been genetically traced to a two human ancestory: A genetic “Adam and Eve”.

Instead, there appears to have been a “mitochondrial Eve” who was the last common female ancestor, and a ““Y-chromosome Adam” who was the last common male ancestor. There is zero evidence that they lived within even 10,000 years of each other, much less than the incorrect notion that they were a mated pair.

For other examples

Did these randomly mutated creatures have to find other similarly randomly mutated creatures to mate with in order to carry on the mutated beneficial gene

The simple answer is “No.” That is a misunderstanding of ordinary biology which is promulgated by any number of antievolutionary outfits and websites. It is simply wrong.

Again, Talk Origins has a very good list of Freqeuntly Asked Questions, and essays which cover this material.

fusilier James 2:24

Basement Activist -

The use of the word “basement” makes me suspect that you may be a parody poster.

Casey’s arguments are bogus.

Therefore there is no God.

Isn’t that what this is all about?

Casey makes an insincere, politically motivated attempt to appease concrete-minded, authoritarian fundamentalists with a logically ludicrous attack on the science that threatens their particular right wing agenda, although it threatens very few peoples’ sincere religious beliefs (not even those of the current hyper-conservative pope, apparently). He is shown to be wrong about science. That’s what this is about. God has nothing to do with it, except to the extent of Casey’s hypocritical claims.

Tim Fuller -

I think the ‘junk’ is just stuff scientists haven’t worked out a purpose for. Of course it’s also possible that nature worked out a way for extraneous DNA to be acquired and really have no knowable greater purpose.

These issues were dealt with in the excellent (and layperson oriented) review by Mike Dunford. Too bad you didn’t read it.

I am somewhat confused on part of the evolution process. Please, claify this for me.

As I understand it, random mutations account for part of our evolution. Did these randomly mutated creatures

Random mutations happen in every organism, including you and me. It is (basically) genes that are randomly mutated; referring to “randomly mutated creatures” is more than somewhat confused. You really should pick up a basic biology book or take a class, so that you will at least know enough to ask questions that make sense.

have to find other similarly randomly mutated creatures to mate with in order to carry on the mutated beneficial gene; or were these mutations of the kind that does not require a like-mutation to procreate?

This is so very confused, and yet could be cleared up by taking a basic biology class or reading just a few pages in a basic biology book. Half of the genes of a child of yours are duplicates of half of your genes (selected at random, more or less), and half of the genes of a child of yours are duplicates of half of your partner’s genes (selected at random, more or less). Except not quite – some of those genes will be mutated – changed – in the process of producing the egg and sperm, so some of your child’s genes will slightly vary from any that you or your partner has. That’s all mutation is, and talk of “require a like mutation to procreate” doesn’t make sense (I suspect you may be mixing up mutations with fatal recessive genes, which are a quite different matter.) If the changes are radical or to some particularly important gene, the offspring usually won’t survive, often not even beyond the one-cell stage. And any “benefit” that a single mutation provides would usually be minute, and there often won’t be any benefit until numerous other mutations have occurred in later generations, and the benefit may not exist until environmental conditions change … the result of random mutations is that there are many slightly different characteristics spread throughout the population (“hybrid vigor”), so when an environmental threat arises, some are better able to deal with it than others, and the changes that allowed that, and thus are carried by more offspring, are beneficial in hindsight.

I have been reading for the last few years now, that there is a consensus among the majority, that humans have been genetically traced to a two human ancestory: A genetic “Adam and Eve”.

If this is true, how is it possible that these two humans, and their immediate offspring (who had to mate with their parent or siblings at first)

Well, you haven’t been reading carefully, or you haven’t read good material, because these two humans lived tens of thousands of years apart and certainly didn’t mate with each other, and the offspring of each of them had plenty of other potential partners; they no more had to mate with their parents or siblings than anyone else does. These two people are simply the last female that is a common ancestor of all humans (Mitochondrial Eve), and the last male that is a common ancestor of all men (Y-chromosomal Adam). That there were such people isn’t just a matter of consensus, it’s a necessary fact of logic in the absence of virgin birth or spontaneous generation – i.e., on the assumption that each of us had one male and one female parent, and each of them had one male and female parent, and so on back at least to the time of these common ancestors. If one were to take a time machine back to visit them, one would find nothing unusual about them – there would be no way to predict that those particular people would be the last common ancestors. In fact, the identity of Mitochondrial Eve and Y-chromosomal Adam can vary from moment to moment, as individual humans die or bear offspring, slightly changing the shape of the genealogical tree. (Note that, even if we’ve misinterpreted all the physical evidence, and the human race is only 6000 years old, descended from the biblical Adam and Eve, the logically neessary fact that there were such individuals still holds, while the assertions that they weren’t unusual and didn’t mate with each other fail.)

The use of the word “basement” makes me suspect that you may be a parody poster.

Odd; I can’t discern any connotation that would suggest that. Do you know what “church basement” refers to? Sometimes you seem particularly clueless about your co-religionists, or in denial, with your frequent “No true Scotsman” arguments. Google “basement activist” and you will find that this person is a real Christian church basement activist.

Like for instance, Behe always predicted IC (irreducible complexity) and IC has not been refuted with anything more than preposterous “just so” stories from naturalists, thus scientifically the IC prediction stands.

How many times has it now been pointed out that (1) IC is in fact a logical prediction made by the standard ToE; (2) The observation of the inevitable production of IC structures was predicted, and made, by Muller about 60 years before Behe came up with it; and (3) IC has nothing to do with ID, despite Behe’s dishonest claims. It’s normal. The only thing to be refuted is Behe’s claim that IC implies design, which has been done ad nauseum.

I also wonder why apparently intelligent people are incapable of being even remotely honest in these matters. When the Real World is so threatening it can’t be addressed with any integrity, this ought to raise a few red flags.

Bond, James Bond -

Since I don’t consider myself a “materialist” and have no problem with “theism”, I’m the perfect one to tell you that, not only are you wrong on every point, but that you are wrong in trivially obvious ways. It’s so tiresome to explain that methodological materialism is a method, essentially a broadly accepted set of common assumptions. I’ll just launch into the specifics.

What’s especially comical is that you fault science for making discoveries. There would be no point in doing science if it “predicted” everything in advance. Hypotheses and theories, once formulated, are tested by predictions.

I strongly suspect you of plagiarizing this list from creationist material, by the way. I also suspect you of hoping to dump so much in one post that no-one would address it, making it seem to go unchallenged. If I am right in either of these suspicions, your honesty is most suspect. Actually, it’s shown to be most suspect several times below.

I also suspect that your true motivations are social and political, and that you make religious arguments to justify a right wing political ideology. Prove me wrong by denying it.

1. Materialism did not predict the big bang. Yet Theism always said the universe was created.

Science, using methodological materialism, if you will, discovered the big bang. Theism made no prediction. Newton was a theist but believed in an eternal universe.

Created by who, Vishnu?

2. Materialism did not predict a sub-atomic (quantum) world that blatantly defies our concepts of time and space. Yet Theism always said the universe is the craftsmanship of God who is not limited by time or space.

Again, science made a discovery. Again, many religious figures argued that the pre-quantum perception of the universe as “perfectly deterministic” in a Newtonian way supported the existence of a divine being. Theism works with either, it makes no prediction.

3. Materialism did not predict the fact that time, as we understand it, comes to a complete stop at the speed of light, as revealed by Einstein’s special theory of relativity. Yet Theism always said that God exists in a timeless eternity.

Again, discovery by science, again, theism does not depend on the speed of light. Nor does the specific question of whether “God exists in a timeless eternity”.

4. Materialism did not predict the stunning precision for the underlying universal constants for the universe, found in the Anthropic Principle. Yet Theism always said God laid the foundation of the universe, so the stunning unchanging clockwork precision found for the various universal constants is not at all unexpected for Theism.

Since human life exists in the universe, the constants and other physical properties of the universe must be compatible with human life. What does this have to do with anything?

5 Materialism predicted that complex life in this universe should be fairly common, Yet statistical analysis of the many required parameters that enable complex life to be possible on earth reveals that the earth is extremely unique in its ability to support life in this universe. Theism would have expected the earth to be extremely unique in this universe.

First of all this is just “god of the gaps”, since neither you nor anyone else knows how much extra-terrestrial life may or may not exist, of even how to define “life”. Second of all, it is a lie if by “materialism” you mean “science”. Some few individual scientists are associated with this view (although what they mean by “common” is not what you mean).

6. Materialism did not predict the fact that the DNA code is, according to Bill Gates, far, far more advanced than any computer code ever written by man. Yet Theism would have naturally expected this level of complexity in the DNA code.

More dishonesty. Why would anyone make such a statement? The fundamentals of the molecular biology of DNA and the genetic code were quite well-understood by the mid-seventies. In fact, the genetic code is simpler and more elegant than was predicted by most, not more complex. Again, science made the discovery.

You don’t know anything about molecular biology.

7. Materialism presumed a extremely beneficial and flexible mutation rate for DNA, which is not the case at all. Yet Theism would have naturally presumed such a high if not, what most likely is, complete negative mutation rate to an organism’s DNA.

It’s hard to patiently deal with lies presented with such smug arrogance. In the first place, the language here betrays your utter ignorance.

With the caveat that the statement is near meaningless, can you provide a source in which science predicted an “extremely beneficial and flexible mutation rate for DNA”?

This really is egregious. No-one who has ever actually learned anything about DNA would write such nonsense, regardless of their religious views.

8. Materialism presumed a very simple first life form. Yet the simplest life ever found on Earth is, according to Geneticist Michael Denton PhD., far more complex than any machine man has made through concerted effort. Yet Theism would have naturally expected this complexity.

No over-the-top lies here, just illogic, and tiresome misuse of the terms “complexity” and “simplest”. Science actually does not yet know the first form of life on earth. Theism makes no prediction; obviously, showing that the first life on earth was simple would not rule out theism per se.

The level of “complexity” or “simpleness” of current life, which is to some degree a subjective matter, does not necessarily tell us anything about the first life, billions of years ago.

9. Materialism predicted that it took a very long time for life to develop on earth, Yet we find evidence for photo-synthetic life in the oldest sedimentary rocks ever found on earth (Sarah Simpson, Scientific American, 2003). Theism would have expected this sudden appearance of life on earth.

Back to lies. Sources, please, and clarification as to what you mean by “long time”, if you wish to prove me wrong.

It’s patently obvious that theism makes no prediction, and can be compatible with any rate of appearance of life.

10. Materialism predicted the gradual unfolding of life to be self-evident in the fossil record. The Cambrian Explosion, by itself, destroys this myth. Yet Theism would have expected such sudden appearance of the many different and completely unique fossils in the Cambrian explosion.

Because this is a complex topic, I’ll refer you to a good link. I expect, based on your arrogance, denial, dishonesty, and lack of adequate background in the life sciences, that you will be unable to make use of it. But I want third parties to see this addressed.

http://www.talkorigins.org/indexcc/CC/CC300.html

11. Materialism predicted that there should be numerous transitional fossils found in the fossil record. Yet fossils are characterized by sudden appearance in the fossil record and stability as long as they are found in the fossil record. There is not one example of transition between major species out of millions of collected fossils. Theism would have expected fossils to suddenly appear in the fossil record with no evidence of transition to dramatically new forms.

Because this is a complex topic, I’ll refer you to a good link. I expect, based on your arrogance, denial, dishonesty, and lack of adequate background in the life sciences, that you will be unable to make use of it. But I want third parties to see this addressed.

http://www.talkorigins.org/faqs/faq[…]itional.html

Materialism did not predict the stunning precision for the underlying universal constants for the universe

A constant is something that doesn’t vary, dude. What’s “stunning” about there being a precise value for something that never changes?

raven on June 24, 2007 3:50 PM (e)

Some of the noncoding DNA questions are empirically addressable. In the study below, the authors just deleted big chunks of DNA and made knockout mice from the cells. Nothing much happened even though some of the DNA was conserved from mice to humans.

Reference from “Jerry” previous thread:

1: Nature. 2004 Oct 21;431(7011):988-93. Megabase deletions of gene deserts result in viable mice.Nóbrega MA, Zhu Y, Plajzer-Frick I, Afzal V, Rubin EM. DOE Joint Genome Institute Walnut Creek, California 94598, USA.

The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially ‘disposable DNA’ in the genomes of mammals.

Since this subject has come up again and again, just going to repost a relevant experiment. Some have pointed out that subtle effects of these deletions might not be detectable under the conditions of the experiment. Formally that is true, I guess. Always hard to prove a negative. But how do you decide whether an effect is too minor to be readily detectable and an effect that is too minor to make any difference?

Actually there are ways to answer this question. Fitness tests. In these experiments mix 25 breeding pairs of the mutants and otherwise isogenic mice together. Check the deletion frequencies over time as the population reproduces. If the megabase deletions have subtle effects on fitness, those alleles should drop in frequency.

The problem with the junk DNA debates is typical of science. There isn’t enough data to answer the question right now except in a provisional and simple minded sense.

When scientists argue endlessly about piecemeal and conflicting data, it means there is not enough data. The solution is to do more experiments and get more data! Been through this many times before and getting more of the required data works very well.

This isn’t done by sitting in a chair either. Someone has to design the experiments, do them, collect the data, analyze it and repeat ad infinitum. Given the complexity and size of the mammalian genome(s), this could take decades.

One way to approach this, would be to do insertion and deletion analysis on mouse populations. The mouse genome seems to be rather plastic with chromosome numbers that even vary between populations by a lot. In addition there are a number of closely related species that are even interfertile. If sequence stretches are lost/gained in wild breeding populations, you can infer that they didn’t have much effect on fitness and weren’t important.

The above is why the DI will always be a fringe group of nonentities. They don’t do science but rather sit on the sidelines and take potshots on real science from a pseudoscientific and ideologically motivated perspective. That isn’t how science is done. All they are is a speedbump and minor nuisance on the road of increasing human knowledge.

For the record, I believe that ID is total bunk, but I also believe any attempt at finding design at the biological level is foolish. Any attempt at finding design should begin at the level of particle physics.

I wonder if this argument over design (based on DNA or observed lifeforms) is just searching for deeper meanings in shallow water?

There will always be the philisophical question of who designed the designer, but if we let go of that (for the sake of argument) and all agree that there is a designer, then wouldn’t the obvious place to look for design be at a level much lower than a biological one? I can’t help but wonder if the ID crowd focuses on the biology part because it’s easier to make false inferences as people have built-in biological prejudices (what, me a monkey??).

It’s also easier to confuse the layperson with biological homilies than mathematical certanties.

Is there a branch of ID that focuses on trying to confuse the physics as much as they do the biology?

Enjoy.

Is there a branch of ID that focuses on trying to confuse the physics as much as they do the biology?

Probably. Science asks the open-ended question “What’s going on here.” ID, like any religious position, asks “How can the observations science makes be force-fit to doctrinal requirements?” These observations might be from any branch of science; all must be vetted (or shaped) for doctrinal purity.

The goal of ID is to find a way to trick the courts into circumventing the First Amendment position on state-supported religion. The current tactic is to attempt to remove the trappings of religion while keeping the substance, so as to be able to tell the courts it’s science and not religion, while simultaneously being able to tell the funding sources that it’s a way to get Jesus into public schools.

Physics mostly tends to undermine fundamentalist doctrine with respect to time scales, and ID tries not to take a position here. Indeed, ID tries to be as minimal as possible with doctrines to make their tent as large as possible. Apparently the latest ID tactic is to take each scientific discovery and claim ID “predicted” it while science did not.

Bond: your last comment was nothing but a re-paste of points you made before. They were conclusively refuted then; and the fact that you re-pasted them anyway (and had them refuted all over again) prove you’re not interested in any form of actual debate or dialogue.

Paul Flocken -

You’ll note that I proactively suggested that he might be plagiarizing, right at the beginning of the thread.

I apologize if this is not the place to ask this question but this is my first post and although I’ve been following the ID/Evo debate here for quite awhile, I’m not sure of the proper etiquette. Anyway…

I understand on the position of those on the side of Evolution that ID is not a “theory” because it is not falsifiable but I have yet to find what it would take (that is, short of “Made by God” stamped on every lifeform)to falsify the “theory” of Evolution.

So that’s my question. Can someone tell me how the TOE could be proven false? I know that there needs to be an answer; otherwise, this would be a case of the pot calling the kettle black! Thanks.

Sorry. The start of the second paragraph should read: I understand the position of those on the…

Dohl,

There are lots of things that could falsify the theory of evolution. That is why it is science. In fact, many of these things could not possibly have been envisioned by Darwin.

For example, based on morphol;ogical and developmental characters, we are fairly confident that the vertebrates represent a good monophyletic group. Therefore, if some vertebrates were more closely related genetically to butterflies and somewere more closely related to jellyfish, evolution would effectively be falsified. However, that has not been found to be the case.

The order of appearance in the fossil record of major groups could also potentially falsify evolution. If for example, vertebrates appeared before bacteria, that would be difficult to explain if evolution were true. Or, (the classic example), if fossil rabbits were discovered in precambrian strata, that would effectively falsify evolution. Needless to say, nothing like this has ever been observed either.

Of course, since the theory has been tested so many times in so many different ways and has not been falsified in 150 years and since the theory has such tremendous predictive and explanatory power, it will take more that just one anomalous data point to falsify the theory now. But contrast that with the ID approach where anything is possible and no designer is identified.

I understand on the position of those on the side of Evolution that ID is not a “theory” because it is not falsifiable but I have yet to find what it would take (that is, short of “Made by God” stamped on every lifeform)to falsify the “theory” of Evolution.

Stanton gave good answers. But that doesn’t mean that I can’t add any.

In truth, I don’t think that “falsification” is especially the issue, and it complicates matters for theories like evolution. Even Dembski purportedly said recently that evolution explains much, which seems like a good way of saying that evolution has the value that we claim for it.

One of the problems with evolution and falsification is that much of what would falsify evolution is collective data. So evolution is falsifiable, but often not with anything simple (I have doubts that even rabbits in the precambrian, without any kind of other evidence against evolution, would single-handedly destroy evolution, since evolution explains everything else).

But that’s said. What would falsify evolution is if organisms didn’t show “family characteristics” across the board. Aristotle and Linnaeus came up with taxonomic categories which actually suggest relatedness (“genus” for Aristotle, “family” for Linnaeus).

Basically, we could start with asking if you had human parents. You’d say yes, and then you’d list the reasons, such as having the same characteristics as other humans (there are other ways, but I’m using this one because it leads us to evolutionary inferences). But I might say, you look different from people in the far north. You’d reply that, sure, there are differences, but the similarities are too great to be the result of coincidence or some such thing.

This is what Linnaeus is supposed to have written (I can’t vouch for it, but it’s attributed to him by many web sources):

“I wish that someone would show me one character by which to place humans and the apes in separate genera. I most assuredly know of none. Had I called humans apes or vice versa I would have fallen under the ban of the Ecclesiastics.”

Actually, we think we have reasonable cause to place humans and apes in different genera. But that’s not the point, what matters is that humans and apes do have “family resemblances”, and this was noted even prior to evolutionary theory (also, it helped give rise to it).

If humans and apes did not have these “family resemblances,” evolution would be a non-starter.

Analogous to this are “textual families” and “related languages”, where we say that one text or one language must have given rise to the later texts and languages, because of the relatedness of these languages and texts. The “original Indo-European language” can even be partially constructed out of its “descendant languages”. In a real sense, our languages evolved, though with significant differences from biologic evolution.

We know, however, that English didn’t evolve like humans and apes did, because its vocabulary is a “fusion” of French and English. Biological evolution has different predictions, like that sufficiently different lineages won’t “interbreed” like French and English did, and thus there will be no viable species coming from chimp-human offspring.

What I’m getting to is that all of the organs and systems of humans and chimps share “family resemblances”, just as you do with your siblings. If you had (non-superficial) bird characteristics, the idea that you had only human ancestors would be falsified. Likewise with humans and chimps, if we didn’t have common ancestors, we’d have traits which weren’t similar, like maybe bird traits. And so:

1. Evolution would be immediately falsified in a lineage if the organism in question were a mosaic of characteristics from various animals (don’t confuse this with “mosaic evolution,” which merely refers to different characters changing greatly at a time when others remain fairly static).

2. Evolution would be immediately falsified if organisms showed the marks of rational design, like machines typically do. Find one organic trait, not modified by humans, which shows design (like a rational leap, instead of gradual modification of inherited traits) and/or a teleological purpose, and you’ll falsify evolution in at least that case.

3. Evolution as understood and in its initial premises would be immediately falsified if life could be shown to have some greater purpose, like doing God’s work, preparing for heaven, or perhaps doing the bidding of aliens (I don’t mean that we’d be enslaved, I mean showing that we were designed for serving aliens). Evolution might still have happened in those cases, but it would have to be either discarded or seriously rethought.

4. Evolution would be immediately falsified if novel characters not related to characters in apparently otherwise “related” organisms were to appear. Let’s say that human bones were made out of carbon nanotubes (almost certainly these could improve bone, if incorporated organically and properly) and every other organism had completely different bones. Humans could not have evolved this, not according to probabilities, and thus could not have evolved if they had this characteristic (though it could be that the other animals evolved).

5. Natural selection would be falsified, as Darwin noted, if an organism were found to have traits and characteristics which exist to benefit another organism without any reciprocal benefit to the first organism. Now understand what I’m saying, my point is not that hosts don’t benefit parasites with their traits, but there, the parasites simply take what they can while hosts typically evolve defenses to that (or die out).

Find some trait that exists for the sake of benefiting other organisms, God, or the good of life in general, and evolution is falsified, at least with respect to that trait.

6. Another way to falsify evolution would be to show that prokaryotes and eukaryotes have the same sorts of relationships across the taxonomic categories, while in fact prokaryotes have vastly different processes of recombination (more promiscuous across the categories, but recombining much less genetic material during each “conjugation”) than do eukaryotes. That is to say, we predict from evolution that eukaryotes will fall into neat cladistic branchings (or “nested hierarchies”) in a kind of “tree”. Prokaryotes will, by contrast, be predicted not to form these neat derivations, but to actually have a kind of mosaic evolution that I said was disallowed above (which it is, but not for all life—and I’m not going to change what I wrote above, because faulting it would be too picky).

So that’s my question. Can someone tell me how the TOE could be proven false? I know that there needs to be an answer; otherwise, this would be a case of the pot calling the kettle black! Thanks.

Well, I’ve added most of my points already. I’d not so much say that any “out-of-place fossil” would falsify evolution (some have been found in unexpected strata, which means that we modify the evolutionary picture, so long as they’re not exceedingly out of place), as that if birds were found before reptiles, fish before cyanobacteria, evolution would be put under severe strain.

I’d like to point out that apparently bogus “human remains” or traces are often trotted out by creationists in order to disprove evolution. Finding genuine human tracks beside genuine (non-bird) dinosaur tracks would indeed falsify present evolutionary theory (whether any could be salvaged would depend on the rest of the evidence), just as the creationists believe.

And if you read UD, they frequently try to show that the “nested hierarchies” don’t work for all traits in all lineages. It’s pretty pathetic, because one simply doesn’t find, say, modern fungi genes in modern humans or anything like that, there are just some remaining questions in the details, not unlike most of science.

If you could really show that a characteristic were impossible to evolve, like my carbon nanotubes in human bones example (impossible in context, that is), that would also falsify evolution. I’m not just repeating myself, I’m leading up to the fact that IDists try to do this constantly with their bogus mathematics and inappropriate models of searches for exceedingly difficult-to-find targets. It is easy to imagine essentially impossible-to-evolve characters, like pterosaur wings on bats, or airplane wings and gasoline motors in humans.

The IDists try to “falsify naturalistic evolution” by claiming that organs, traits, and systems that are related across vast numbers of organisms, essentially could not evolve. And yet none of these is without the marks of an evolution indistinguishable from “microevolution” in its essential aspects, nor are there any obvious breaks between what they claim is “designed” from what is “evolved” even in their own minds.

Generally, evolution would be falsified by breaks in evolutionary continuity, whether in the fossil record, in morphology, in the genes, or in the correlations between all of these (the correlations understood according to the difficulties of finding fossils in some cases, of course). Just find anything that breaks the expected patterns of evolution, like novelties underived from anything else, fossils wildly out-of-sync with genetics, or mosaics of separate vertebrate lineages, and you’ll have falsified evolution in at least one area in which it is claimed to work.

I repeat that we wouldn’t have “creation scientists” or “intelligent design advocates” if both of these strains of pseudoscientists didn’t recognize that evolution doesn’t have falsifiable aspects to it. Various creationists, like Lord Kelvin, tried to show that evolution was falsified because there wasn’t enough time for it, but astronomical dating, radiometric dating, and a host of processes which yield indeterminate yet long dates for the earth have borne out the predictions of evolutionists (and of most geologists) that the earth must be at least hundreds of millions of years old.

The problem for these people isn’t that evolution isn’t “falsifiable” in the Popperian sense, it is that it cannot be falsified by the data available. Sometimes these people conflate the fact that the data can’t falsify evolution with the concept that evolution is “unfalsifiable”. But they couldn’t even hope to make their case against evolution if it were unfalsifiable in Popper’s sense, and they may as well not whine when they can’t find anything that isn’t consistent with evolutionary predictions.

Glen D http://www.geocities.com/interelectromagnetic

I’d like to add another four theoretic falsification possibilities for evolution, because they are among the best for anyone who isn’t steeped in biological knowledge.

1. Evolution would be falsified if there were no vestigial organs. This isn’t a favorite “argument” in general any more, partly because some incautious evolutionists “found” lots of vestigial organs, plus we’ve mostly moved beyond those matters in evolutionary research.

But even though vestigials might naively be expected to disappear rather quickly once they really were vestigial, evolution under the constraints of shared developmental processes across organs and traits would continue to predict that at least some vestigial organs would exist. And they do. Juvenile platypus teeth, the coccyx in humans, and the teeth of young baleen whales are some of these. The fact that there might be some function among these does not change the fact that they are essentially useless in the functions that related organisms have for them.

We’re lucky that we have platypus teeth, however, because they are important to show the relationships between platypus ancestors and the modern species. Just another thoughtful aspect of this world from the “designer”;):)

2. Evolutionary relationships would be revealed in the developmental programs of organisms, or evolution (under known constraints) would be falsified. Haeckel’s claims have long been exploded, of course, but we still get claws on the wings of some birds while they’re still in their eggs (and in juvenile hoatzins), humans have many similarities with our ancestors at a certain stage of development, including the tail that turns into our vestigial coccyx, and the testes in most mammals have to descend (before birth in humans, after in some mammals) into the scrotum from the ancestral position in the abdomen.

3. And evolution would be falsified if no transitional fossils could be found. This is a prediction involving the collectivity of data, and the lack of a transitional for, say, gibbons would not be devastating, both because gibbons fossilize poorly (wet forest environments) and because we don’t bother looking much for gibbon fossils.

But among reasonably easy-to-fossilize organisms, transitional fossils would be predicted to have been found by now, and they have been found for all of the “class transitions” of vertebrates. So, for example we have transitional forms for the evolution of birds, amphibians, and mammals. Likewise for hominins, rhinoceruses, whales, horses, and many plant classes.

Again, this brings up one reason why I have issues with falsification as “the standard”, though I often resort to it as shorthand as well in calling for ID to follow normal science standards (I also don’t like it because it takes the emphasis away from induction and positive evidence). It isn’t that a particular observation, or lack thereof, would falsify evolution, but that in the present context we’d expect to have found many transitionals, and we have. It’s a probabilistic version of “falsifiability”, not the direct “deterministic” sort of falsification is all that many know of.

4. The following falsification standard relates to previously-mentioned vestigials, evolutionary constraints, and the marks of design, but I’d also mention that if everything was more or less “optimally” designed, evolution would be immediately falsified. Or even if we didn’t hold the organic world to standards of perfection, at least we could say that if everything was built as well as, say, the latest and best computer chips are, that would falsify evolution.

Instead we have a variety of problems in the biological realm, including the fact that no large leaps to better materials (like synthetic composites) are possible, the eye has its blood vessels on the wrong side of the retina (despite IDist claims to the contrary, it is not fully compensated, or optimal—otherwise birds wouldn’t evolutionarily minimize this defect) due to inherited developmental constraints, and vestigials exist.

5 (okay, I just thought of this one, so it’s not “four” any more). Additionally, transitional forms are quite obviously not as well adapted as “later models” are, so that clearly archaeopteryx labored under difficulties that later birds do not have. Yes, once again the prediction of evolution, in this case that later forms of an inherited trait will generally be better than the earliest-found forms, is borne out by the evidence.

You could falsify evolution, then, by showing (in a line which has many fossil representatives through time) that the first representatives of a complex integrated ability like flying are as good at it as the versions found tens of millions of years later. Where we have clear examples, like flying, or walking in the amphibians, the earlier versions indeed are poorer at it than later organisms are, such as the swift and the cheetah.

Glen D http://geocities.com/interelectromagnetic

Well, that latest comment was more like the “old” Glen for length, but was intersting and well-said nonetheless.

As pointed as Stanton’s more succinct reply, just with more point and sub-points.

(If my old eyes yet serve me, however, Stanton meant to reply to “Doh!” and not to “Dohl.” Which leads me to speculate that Stanton may have old eyes as well.)

Steviepinhead,

You are correct sir. However an equally plausible hypothesis might be that my right hand knoweth not what my left hand doeth.

I ruled out the fumbled-finegered-typist hypothesis based on the impeccability of the great bulk of your prose as posted here.

I am, of course, always willing to revise my hypotheses when presented with additional, conflicting data.

Of course, just to make others feel better, I always include at least one *deliberate* typo in any post that touches, even glancingly, on typing ability.

In the above case, this inclusion was “finegered” for “fingered.”

Note, however, the rule “at least one.”

If you note others, you may be sure that they, too, were *deliberate.*

Doh! -

When the theory of evolution first became prominent, almost nothing was known about biochemistry. Genetics was not yet understood at all. The role of DNA was not even understood. It was not completely accepted that microbes could cause infectious disease! Many other very basic things were unknown.

We have been learning more and more about life for 150 years. Each new thing we learned potentially could have caused problems for the theory of evolution, but each new thing we learned - biochemistry, cellular biology, electron microscopy, molecular biology, etc, etc, etc - continued to support the theory of evolution.

ID offers nothing. If life shows signs of common descent it’s “common design”. If common descent is ruled out, it’s “individual design”.

Here’s a helpful link…but before you click it, please answer a question for me.

Do you care? Or were you just mouthing what you hoped would be a creationist “gotcha”? Do you give a damn what the evidence actually shows, or are you dedicated to creationism, the hell with the honest evidence?

http://www.talkorigins.org/faqs/com[…]ection1.html

I like Glen’s list. And he’s right, if no transitional fossils had ever been found, that would be a huge problem for the theory of evolution and would probably be enough to falsify it. Of course that one has kind of gone by the wayside. We can’t really undiscover the fossils at this point, so ignoring them will have to do for some.

However, we have yet to sequence even a single gene from most known organisms. (That is in fact the goal of the Barcode of Like Database project). Since there is so much work to be done, and since there are so many possible opportunites to disprove evolution, you would think that the ID crowd and creationists in general would be pumping huge sums of money into automated sequencing efforts. I wonder why they don’t seem to be doing that?

As for junk DNA research, why bother when no matter what anyone else discovers you can always claim that you predicted it?

Doh!– I hope you reply back, because people have put a lot of effort into answering you. Taking the theory of evolution from an historical perspective, keep in mind; 1. The Genesis story was already in trouble as a scientific theory before Darwin wrote word one of The Origin of Species. The real doubts mostly came from geologists, not biologists, but scientists were flailing around, trying to make sense of layer upon layer of stone that looked like it had been laid down over a long time, not thrown together in 6 days, and then churned up in a flood. If this hadn’t been true, Charles Darwin would be long forgotten. 2. The theory of evolution hasn’t been disproven– but not for want of trying. After OoS came out, practically everybody took a shot at knocking down evolution. The ToE came through each challenge stronger than ever. The “disproofs” of the current creationists are often steals from respected 19th-century scientists. Can you blame modern scientists for ignoring issues that were settled over a century ago? 3. The fact of evolution has become more and more apparent over the years– but Darwin’s actual theory has been proven wrong in many, many particulars. If scientists were interested in replacing God with Darwin, why would they be perfectly happy to throw large chunks of his conclusions out the window? In fact, most evolutionary biologists and geologists working today don’t care one way or the other about what Darwin said. They base their research proposals on the work of their immediate predecessors, who based their work on their immediate predecessors.… And so on. If, at any iteration, solid evidence had come out against evolution, hordes of researchers would have jumped in with glee. It never happened. So, sure, in principle evolution could be disproven. But in practice no legitimate scientist sees any way to do this. They don’t reject ID or ‘scientific’ creationism because they don’t like its conclusions– they reject it because it’s not science. It may look like science to a naive outsider, but to real scientists trying to run research programs, there’s simply nothing in creationism but misstatements and faulty logic– nothing at all a researcher can use.

I know what you’re talking about, and my undeniably subjective memory is quite different.

Unlike you, I don’t conveniently depend on my subjective memory to maintain intellectual dishonesty, I go back and read the posts. You would do so if you had anything like the integrity you pretend to.

Again, memories differ. Your posts are usually on topic and relevant, and the “insults” contained therein are usually mild, comical, and deserved. When you have taken me to task, you’ve always had a valid point. That is not my recollection of the other poster you refer. Again, I could be experiencing self-serving bias here, but I don’t think so.

Sheesh, Harold, are you really that dense? Apparently only when it serves your intellectually dishonest purposes. You are trying very hard to draw a distinction between two people who are in fact the same person.

What I’m saying is, sheez, how can anyone compare PG to Lenny? It has to be on about the same order as comparing modern evolutionary theory to ID.

Thanks for saying so.

Obviously, as can be deduced by my prior posts, I don’t agree that Lenny’s phrases were hackneyed.

You’re just waving your dick around. (shrug)

I recall that particular poster as becoming obsessed with my posts, not the other way around

It’s fascinating how people enshrine their own previous self-serving expectations in their memory as if the expectations were the actual facts:

http://www.pandasthumb.org/archives[…]omment-43234

But I think there’s more to it than that. Harold, as Lenny did (but not by name) has now called for me to be banned — hey, I might vote for it myself; I obviously spend way too much time here. But it’s interesting that both Lenny and Harold first developed their animostiy toward me in the same conversation, one in which Lenny kept repeating the same challenge over and over, to use the scientific method to answer whether murder is wrong, even after I had agreed that’s not possible but that it wasn’t a refutation of what I and Don P had said, which was that science can address anything in the world. And the dispute with Harold was about science and religion — but this was in an old thread where no one other than Harold, Lenny, Don P, and I were posting, not like these recent threads where the article topic was explicitly about religion. Anyway, Harold got extremely emotional and wrote a long rant about what a horrible human being I am. When I referred to that as “an ad hominem rant”, he insisted that it wasn’t and went into another rant about people like me accusing others of ad hominems and even that we always use that phrase (a weird complaint) and predicting that I would follow him around here and insult him — which of course I didn’t, but he did try a few times to bait me. That seems to me rather pathological.

Here is some more grist for the recollection mill. Reading it over, I have the same view of your dishonesty at the time as I did then.

She’s pretty average…definitely better than Beyonce though. I noticed one of her songs sounds almost exactly the same as another song a male pop band does.…buuuuut i cant remember what the song is atm!!…but does anyone know what I’m talking about? lol

About this Entry

This page contains a single entry by Mike Dunford published on July 16, 2007 11:42 AM.

Forrest and Gross: Biochemistry by design was the previous entry in this blog.

Be a scientific consultant for the Clergy Letter Project! is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.381

Site Meter