Does ID predict genetic similarity?

I'm pretty sure I agree with your reasoning over all, but a quick question:

When you say "genetic code" do you really mean "genetic similarity"? E.g., "Researchers are finding that plants that were once thought to be closely related cannot possibly be because there is too much difference in the genetic code" - does this mean that the actual genetic code is different or that the DNA sequences are substantially different?

Since I'm one of the few ID proponents left around here, I'll offer my thoughts on this post soon, herebedragons.

Nice thread by the way.

Here are my thoughts on herebedragons's post.

In the first place, ID as a concept is so loosely defined that one cannot say what it predicts at all.

For example, the "mainstream" ID community (e.g., the Discovery Institute) defines intelligent design in this manner:
"The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection."

However, this "theory" encompasses quite a lot, from cosmology to biology. Furthermore, it is not at all rigorously defined, which - as I stated previously - means that you can't make any real predictions.

Thus, if someone says that ID does or does not predict nested hierarchies in biological organisms, you would first have to define ID.

For example, the view that all species were intelligently designed doesn't predict a nested hierarchical pattern based on DNA sequences. On the other hand, front-loading does predict this precisely because it incorporates both intelligent design and evolution. In short, if we didn't see this nested hierarchical pattern in DNA sequences, front-loading would be effectively falsified (and so would the current theory).

While the global concept of ID doesn't make any true predictions, specific ID hypotheses do make testable predictions. For example, the ID hypothesis that "irreducible complexity can only arise through intelligent intervention" is quite testable. The hypothesis would predict that there are no non-teleological pathways to IC systems.

Conclusion:
Before we can make any statement about what ID predicts, ID as a scientific hypothesis must first be adequately defined.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.

Do you have any other ideas as to what predictions ID makes (in particular as compared to common descent)?

As I said above, ID as a concept doesn't make any predictions because it is so loosely defined. But I think that ID hypotheses do make testable predictions, and predictions that common descent does not make. For example, I've been fleshing out the details of a "rational design hypothesis" for the engineering of molecular machines, a hypothesis which I believe makes testable predictions. Some of my thoughts can be found in the Nature's Engines and Engineering thread.

Do you have any other ideas as to what predictions ID makes (in particular as compared to common descent)?

As I said above, ID as a concept doesn't make any predictions because it is so loosely defined. But I think that ID hypotheses do make testable predictions, and predictions that common descent does not make. For example, I've been fleshing out the details of a "rational design hypothesis" for the engineering of molecular machines, an ID hypothesis which IMHO makes testable predictions. Some of my ideas are summarized in the Nature's Engines and Engineering thread.

I know I have said this before, but one of my major disappointments with the ID movement is that it primarily focuses on finding flaws in the current biological paradigm instead of working on presenting a rigorous, testable ID hypothesis.

Ewps, a duplicate post. How embarrassing. Moderators, feel free to remove the older of the two posts.

And yet no ID proponent or creationist would ever accept the argument that examples of unorder and unsystematic, or seemingly illogical choices, that might be indicated as consistent with evolution, are counter examples to a designer or creator.

I am just one such ID proponent: if a biological system displays property of irrational design, I count that as one point against the thesis that that system was engineered. But the road must go both ways. If a biological system displays properties of rational design, then that is a point in favor of viewing it as engineered.

Yet in Inside the Human Genome: A Case for Non-Intelligent Design John C. Avise uses 240 pages in arguing that the genetic design flaws in humans is a strong counterpoint against ID. Similarly, this same biologist has authored a paper in PNAS entitled "Footprints of nonsentient design inside the human genome" and concludes:

"From scientific evidence gathered during the past century, and especially within recent decades, we now understand that the human genome and the metabolic processes it underwrites are riddled with structural and operational deficiencies ranging from the subtle to the egregious. These genetic defects register not only as deleterious mutational departures from some hypothetical genomic ideal but as universal architectural flaws in the standard genomes themselves. The findings of molecular biology thus offer a gargantuan challenge to notions of ID."

But if flawed design is evidence against ID, then rational design is evidence for ID. Would Avise accept the argument that since the core structure of the bacterial flagellum - or the ATP synthase, for instance - displays properties of rational design, then these systems show signs of intelligent design?

Nobody knows what the characteristics of a designed biological system are. Instead we have things like 'I know it when I see it', specified complexity, and irreducible complexity which are attempts to say 'order' == design.

You misunderstand irreducible complexity. The IC argument never was order = design. Just saying.

If we could provide a scientific methodology for identifying such characteristics, we would be on our way to making ID scientific.

Alternatively, we could make specific ID hypotheses about the biological world and see how the predictions of these hypotheses match up to reality.

Nope. That's simply not the case.

Yes, it is. If you argue that flawed design is a point against ID, then the opposite must necessarily be true.

What do you mean by "point".

I simply mean "argument" in this context.

Your argument is flawed, and much of the discussion I see in this thread attempts to hammer away at the error you state here explicitly. I had avoided supporting my statement because I had thought the reasoning behind it is obvious. But in face of a "Yes it is argument" I provide the following example. I might postulate for example, that iron based blood cells indicates a designer who copied his own biochemistry. Prevalence of iron based blood is absolutely required by my postulate. Accordingly, counter-examples are particularly damaging to my "argument". Yet, given that the mechanism for transporting oxygen through the body and releasing it where it is needed is highly dependent on iron, that iron is a common element in the population II/III solar systems and on earth, and the ready availability of oxygen as a participant in energy releasing systems, we can easily come up with alternative reasons for why iron based blood chemistry is prevalent.

You did not address my argument at all in the above. My argument is that if one argues that bad design is evidence against ID, then rational design is evidence in favor of ID. Instead of addressing this point, you went off into a tangent IMHO.

Let me put it this way: why exactly is poor design of a biological system an argument against the engineering of that system? The standard evolutionary explanation for poor design is that evolution works as a tinkerer instead of an engineer. But then we find that at the same time evolution can work as an engineer. This means that both poor design and optimal design are compatible with Darwinian theory. Of course, this comes at a price because there is a loss of predictive power.

On the other hand, it is often argued that suboptimal design is evidence against engineering because engineering should not produce such suboptimal design. Thus, from an ID perspective, if we hypothesize that a given biological system was engineered we would predict that further study of that system will reveal that it is indeed optimally designed. Does that make sense?

Whenever someone asserts that if a proposition is true, the inverse of a proposition is also true, I know immediately that the argument has a flaw. The conclusion may be correct, but is unsupported by the argument. Your argument regarding evidence does exactly that.

It is quite obvious that if a proposition is true the inverse of that proposition is not necessarily also true. E.g., I breathe when I sleep is not the same as I sleep when I breathe.

Nonetheless, the statement that poor design is an argument against ID does imply that rational design is an argument in favor of ID. Engineers generally do not produce suboptimal designs, and instead produce rational designs. Thus, the presence of rational design in a biological system is a hallmark of intelligent design, and one that would allow us to make further predictions.

Loads of problems with this argument, the obvious one being why a godly designer would have ANY bad design at all?

As soon as you step into the question of a why a divine designer would have any bad designs, you have left the realm of science and entered that of theology.

Given that it is not my position that a god designed features of life, your objection is not particularly relevant for me.

I'm afraid you are always going to be pushed back into philosophy because saying that the design for life was not divine begs the question of how the non-divine creator came about.

This question is easy to answer:

1. That the first genomes on earth were designed in no way implies that the intelligence that designed these genomes was also designed. This is because we have only limited knowledge on the scope of intelligence. I.e., there are many possible forms of intelligence that could exist, including non-biological intelligence. We have little information on how intelligence originates because the only intelligence we have experience with is biological intelligence (and AI). For example, it is possible that some intelligence exists that consists solely of different patterns of electric impulses and currents. This is the theme of Arthur C. Clarke's story "Crusade": a planet bathed in extremely cold seas of helium is an ideal environment for the origin of electrical intelligence because electric currents can run forever (given that the helium functions as a superconductor). Thus, electric currents run throughout this planet, and over time they evolve into a computer intelligence. The story goes on, of course, but the point is this: certainly, even if our own biological life could not have plausibly evolved, it is possible that other forms of intelligence exist which could evolve. The argument that "saying that the design for life was not divine begs the question of how the non-divine creator came about" is therefore deeply flawed IMHO. There is an easy solution to this question, as explained above.

2. Also, the question is a bit irrelevant to me because, for the most part, I'm trying not to argue for ID based on the implausibility of evolution but rather based on positive evidence for ID. In other words, it is perhaps possible for non-teleological processes to produce life but this does not mean that these processes did produce life. When discussing biological origins, it must be remembered that we are talking about actual history and not about what could have been. As I explained in a previous thread:

The intelligent design/evolution discussion has somewhat ignored the historical nature of biological origins. By this I mean that ID proponents have focused on demonstrating that biological system X could not have evolved through Darwinian mechanisms, instead of asking the simple question: did biological system X actually evolve or was it intelligently designed? In other words, the discussion over biological origins has essentially become a question of plausibility, rather than a question of what actually happened. Biological system X could plausibly evolve but this does not mean that it did. The human mind is quite capable of imagining very creative non-teleological scenarios for the origin of any biological system, and we have to take this into account when considering the origin of a given biological system. A statement of plausibility says little about what actually happened in the history of a system, and thus independent evidence is needed to support any conclusion, be it non-teleological or teleological. We need to emphasize the historical nature of biological origins and instead of endlessly arguing over the plausibility (or lack thereof) of evolutionary mechanisms, we should try to determine what actually happened in the past.

Thus, if evolution could possibly account for the origin of the first genomes on earth this does not translate into what happened in the past. And if the evidence points to ID having played a role in the origin of the first genomes then this is what actually happened, but this does not mean that the origin of the first genomes requires intelligence - and this, in turn, means that evolution could account for the origin of the initial intelligence.

(It should be noted that I do question the competency of non-teleological processes to explain the origin of certain biological systems, but this isn't where my focus is)

In summary, the argument that ID necessarily leads back to a deity is not at all rigorous and makes several problematic assumptions.

That apart, a point based system based on good and bad design features in nature in order to provide evidence for a designer isn't going to get you anywhere either, simply because with evolution, better design wins over poorer design - so the result is the same.

I'll respond to this bit in a future post, but the for the moment let me offer this comment: by the above argument it appears that evolution does predict that good design in systems rather than both good and bad design because "better design wins over poorer design - so the result is the same." Yet we see many instances in the biological world of inherently flawed design, which I think is an effective response to the quoted statement above.

Edited by Genomicus, : No reason given.

I disagree. Your response is not effective.

Only because you're misinterpreting it.

For example, I never argued that evolution predicts that biological systems will be optimally designed, contrary to what you imply. What I did argue is that if we accept Tangle's argument that "better design wins over poorer design - so the result is the same," then it seems as if evolution would predict that biological systems will be optimally designed. However, since Tangle's argument is not correct (and assuming I'm interpreting in the right way), evolution makes no predictions regarding optimality or lack thereof.

The 'easy' answer is to imagine another form of life that can wish itself into existence [note: I didn't say this intelligence could wish itself into existence did I?]. This life form is non-biological but can make something biological and trasfer it to another planet for no obvious reason. And your evidence is a science fiction novel?

For some odd reason you completely ignored the parts that I bolded, where I emphasized that it is possible that non-biological intelligence can exist and evolve. Given that this possibility is no more outlandish than the existence of a god, there is no reason to assume that if biological life requires design, then the intelligence behind our biological life likewise requires design, forcing us to backtrack up to a deity.

Of course I'm not citing a science fiction story as evidence, and I think you know that

That merely served to illustrate my point - a point which IMHO you basically ignored. Please respond specifically to my point, which is as follows:

1. You argued that intelligent design, philosophically, will always lead us back to a god.

2. I responded that this is incorrect because there is the possibility of a non-biological alien intelligence existing that does not require intelligence in order to originate, and if we accept this possibility, then ID does not necessarily require the existence of a deity.

Edited by Genomicus, : No reason given.

But nature is rarely a straight fight and evolution is not remotely interested in optimising - it's very happy with good enough and make do and mend. And when some feature is no longer under survival pressure, practically anything will do. We have stacks of evidence for this from junk DNA to vestigial organs and the inverted retina (above).

Yes, I know you have stacks of evidence for flawed design, but at the same time there are stacks of biological systems that, at their core, clearly display rational design and show no signs of flawed design.

So you need to explain why a designer would design badly and why it would do it in such a way to make it look identical to how evolution actually does it.

Alternatively, I could take the approach that poor design counts against the design inference, which means that design probably wasn't involved in the origin of that system.

That is indeed true. And you have ignored the small problem that this imagined non-biological intelligence has to create a biological organism and transport it here some 4bn years ago.

Do you admit that this is a possibility? If so, your argument - that ID necessarily forces us to a deity in the end - is rendered invalid IMHO.

The problems you see with the designer I outline are certainly valid, but they are not particularly relevant to one specific point: if it is possible that such an intelligence can exist and design biological life, then ID does not necessarily trace back to a god.

On what grounds do you say that your hypothesis is no more outlandish' than a deity? I find it barking mad and I don't believe in a god. We have better local solutions, why search for the absurd...No, it requires something far, far, far more unlikely.

Your statement that my little idea (which, incidentally, I don't believe in - I'm simply pointing out that your argument isn't valid) is far, far, far more unlikely than a god is entirely a subjective one. There are plenty of atheists who will say that the idea of a god existing is much more barking mad than the idea I have outlined.

I don't think you're adequately supporting your contention that ID necessarily requires there to be a god at the start of all of it - your only argument seems to be, for the most part, one of personal incredulity.

Again, my idea is simply to demonstrate how flawed your argument is.

One more point:

And it's totally unecessary when we have mechanisms that don't require your added improbability.

Whether an intelligence is necessary for abiogenesis or not is another subject, of course. But a common argument is that since ID says that intelligence is required for biological life to originate, then ID necessarily requires a god. This is not the case, as I have demonstrated by the little thought experiment of a non-biological alien intelligence.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.