At a thread at another website discussing the idea that ID is “boring”, an ID supporter wrote this:

“[ID] is boring to Will [Provine] I suspect (and to others for the same reason) because they rule out the possibility of an intelligent designer.”

Actually, knowing Will Provine pretty well and hearing him say that ID is “boring” on several occasions, I can confidently state that the reason he finds it “boring” is that whenever something interesting in biology is discovered and somebody asks “Why is that thing the way it is?” Will hears most ID supporters answer “Goddidit”. His opinion of ID is that it’s a science-stopper because rather than suggesting new and interesting ways of trying to figure out how something came to be the way it is, he thinks that IDers simply throw up their hands and say “It’s too complicated, so God / the Intelligent Designer must have done it”.

Personally, I don’t find ID boring for quite the same reason, as I don’t always see ID supporters resorting to the “Goddidit” pseudoexplanation. No, the reason I tend to find most ID boring is it’s relentlessly negative. That is, people like Michael Behe and William Dembski observe something marvelously complicated and say “That’s Irreducibly Complex!” or “That’s Complex Specified Information, so it couldn’t have evolved via naturalistic means”…and then they leave it at that. No alternative means of creating the marvelously complicated thing is proposed (unless you credit Behe’s “puff of smoke” pseudoargument).

Furthermore, I generally don’t see ID supporters doing any original empirical research. In particular, I don’t see any of them going out into the field (my favorite place to discover things) or into the lab and “getting down and dirty” with some biological phenomenon that they find absolutely fascinating.

My friend, Harry Greene (the world’s authority on rattlesnakes) is my idea of a real scientist. He absolutely loves snakes, talks about them at the drop of a hat, has spent his entire professional life studying them in the field and in the lab, and has revolutionized our understanding of the ecology, ethology, and evolutionary biology of reptiles. To me, he’s the epitome of an evolutionary biologist, because he has what we call “a feel for the organism” which goes far beyond simply studying it as an experimental subject.

And my friend, Lynn Margulis (the world’s authority on endosymbiosis) is also my idea of a real scientist. She absolutely loves getting knee-deep in the mud of some tropical lagoon and scraping scum off of rocks to look at under the microscope. She’s spent her entire professional life studying microorganisms in the field and in the lab, and has revolutionized our understanding of the evolutionary biology of microorganisms. Like Harry, she’s the epitome of an evolutionary biologist, because she also “a feel for the organism” which leads her to discover things nobody ever thought to look for before, such as symbiotic bacteria embedded in the cell membranes of symbiotic protozoa from the guts of termites.

I have yet to meet or hear about or read about any ID supporter who does anything like what Harry and Lynn do. Yes, Michael Behe is a biochemist, but the things he does in his laboratory at Lehigh have little or nothing to do with ID. And William Dembski wouldn’t know an actual living organism if it lunged out and bit him on the ankle.

Biology, and especially evolutionary biology, is that branch of the natural sciences founded and maintained by people who loved and were obsessed with nature and natural things. Darwin and Wallace and Fisher and Haldane and Wright and Dobzhansky and Mayr and Simpson and Stebbins and Hamilton and Trivers and Margulis and the two Wilsons (Edward O. and David Sloan): these are my heroes, and they are the “naturalists” (see how the word has another, much more positive meaning?) who have been the inspiration for my research, insignificant as it is compared with theirs.

And all that IDers can generally do is say “No, you’re wrong, it can’t happen that way, in fact it can’t happen at all without a deus ex machina?” Ugh: boring, pointless, and most of all, no “feel for the organism”.

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As always, comments, criticisms, and suggestions are warmly welcomed!

–Allen

Mike Gene, the pseudonymous founder of Telic Thoughts and the author of The Design Matrix: A Consilience of Clues has written the following about metaphors and their application to the detection of intelligent design:

Metaphors such as “fear”, “cost”, “abhor” and “angry”, commonly share the projection of consciousness onto the world. Metaphors such as these represent the human tendency to view the world through anthropomorphic glasses. However, the metaphors employed by molecular biologists are not of this type.
…
Metaphors typically break down when we begin to take them literally.
…
[but] The design terminology that is used in the language of molecular biology does not break down when interpreted literally
…
[T]here is a basic and literal truth to the use of design terminology in molecular biology–these technological concepts are just too useful. Metaphors are certainly useful when explaining concepts to other human beings, yet the design terminology often goes beyond pedagogy–it provides true insight into the molecular and cellular processes. An understanding of our own designed artifacts, along with the principles required to make them, can guide the practice of molecular biology.

Metaphors are a special case of analogies (the other being similes). I have written extensively on the subject of the use of analogies and metaphors in science, and especially in the evolution/design debate here, here, and here. The fundamental question in this ongoing debate is, how do we know an analogy really exists? For example, do we have any objective way to determine if one rock is analogous with another? Or whether an anatomical feature (or a protein/substrate binding site) is analogous to another?

As in the case of agency detection, we think we can do this very easily (just as we can easily identify what looks like design), but I would argue that this is because both “finding” analogies and “finding” design and purpose are capabilities of the human mind (and the nervous system that supports it) that have conferred enormous adaptive value on our ancestors. As in the case of our hypothesized “innate agency/design/purpose detector” (which first becomes active in very early infancy), our “analogy detector” also appears to become active at a very early age, and operates entirely in the background. That is to say, we are almost totally unaware of its operation, and concentrate only on its output.

Our ability to detect (and construct) analogies is, IMO, the core of our intelligence, as demonstrated by the fact that identifying analogies has been traditionally used as one of the most sensitive gauges of general intelligence in intelligence tests (such as the Miller Analogies Test).

In the context of Mike Gene’s ideas about metaphors, doing engineering (and especially mathematics) is essentially the construction of highly compact analogies, in which numerical (and sometimes physical) relationships are expressed in the form of abstract symbols. A blueprint is simply a metaphor for a building, just as a chemical formula is a metaphor for the product of the chemical reaction, and a recipe for a cake is a metaphor for the cake. Indeed, many mathematical relationships (especially in the natural sciences) are expressed as equations, which are quite literally metaphors expressed in symbolic form. For example, Newton’s equation for force:

F = ma

is a metaphor linking the concept of force with the concepts of mass and acceleration.

In molecular biology we encounter once again the concept of metaphors, for what is the genome of an organism but a highly abstract metaphor for the fully embodied and operating organism itself? I agree with those (and I expect Mike Gene would number himself among them) who assert that the encoding of “life” into a string of nucleotides is indeed the crucial difference between biological “metaphors” and physical “direct necessities”. Gravity isn’t “encoded” in anything, but proteins are, and so are cells, tissues, organs, organ systems, organisms, and (at least at some level) their behaviors.

So, is there a way to verify if an analogy or metaphor is “real”? In the case of some analogies in biological systems we have an independent double-check on our identification of analogies. This is based on the evolutionary concept of homology, or derivation from a common ancestor. If two structures on two different organisms (say a small bone of the jaw of a reptile and the even smaller bone in the middle ear of a mammal) appear to be analogous (on the basis of size, location, relationship to other bones, etc.) there are at least two different, though related, methods of verifying that these structures are indeed analogous (and not just accidentally similar).

One way is by means of comparative paleoanatomy, in which a series of fossils of known age are compared to determine if there is a connection between the evolutionary pathways of derivation of the structures. If such a pathway can be empirically shown to exist, this would be strong evidence for both the analogous and homologous nature of the objects.

Alternatively one could compare the nucleotide sequences that code for the structures to determine if they are sufficiently similar to warrant a conclusion of homologous derivation. In both cases, evidence for homology, combined with our intuitive “identification” of analogous structure and/or function, both point to the same conclusion: that the two structures are both analogous and homologous.

This is why structures that appear to be analogous, but for which there is no convincing evidence of homology (as in the wings of birds and insects) can present a serious problem to evolutionary biologists, and especially those engaged in biological classification. Such apparent similarities (technically called homoplasies) can either be the result of “true” (i.e. partial) analogy at the functional (and/or structural) level (and therefore assumed to be the result of convergent evolution) or they can be completely accidental. Simple inspection is often insufficient to separate these two hypotheses, and lacking either fossil or genomic evidence, conclusions about the validity of such analogies can be extremely difficult to draw. However, if there is fossil and/or genomic evidence and it points away from homology (i.e. descent from a common ancestor), then the structures can be considered to be analogous, but not homologous.

One of the dangers in invoking analogies and metaphors is overusing the concept of analogy to mean almost anything. Indeed, it is essential in discussions such as these that we be as precise as possible about our definitions, as imprecision can only lead to confusion (at best) and unsupportable conclusions (at worst).

Perhaps the most essential distinction to be made in this regard is between “analogies of description” (which could also be called “semantic analogies”) and “analogies of function/structure” (which could also be called “natural analogies”). The former (i.e. “semantic analogies”) are merely artifacts of the structure of human cognition and language, as happens whenever we describe an analogy that we have perceived.

By contrast, the latter (i.e. “natural analogies”) are the actual similarities in function/structure that we are describing (i.e. that resulted in our identification and description in the first place). As in the Zen koan about the roshi and the novice in the moonlit garden, much of the confusion about which of the two types of analogies we are discussing seems to stem from confusion between the moon that illuminates the garden and the finger pointing at the moon.

In the brief example from Mike Gene’s The Design Matrix posted at the head of this thread, the implication is that the analogies we perceive between biological systems and those engineered by humans are “natural analogies”; that is, they are real analogies, and not simply a form of linguistic convenience. However, there is nothing about the finding of an analogy that necessarily verifies that the analogy is “natural” (i.e. “real”), as opposed to “semantic” (i.e. “imaginary”). This would be the case even if one found repeated analogies between complex systems engineered by humans and biological systems that evolved by natural selection. To verify that an analogy is “natural” requires an independent source of validation for the assertion that the analogy is “real” and not merely “semantic”. At this stage in my reasoning about this subject I am not at all sure how one would go about this.

However, one thing I am sure of is that simply asserting over and over again that one has perceived an analogy, and that this is all that is necessary to validate the analogy, is not sufficient. Even I am but mad north-north-west: when the wind is southerly I know a hawk from a handsaw.

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As always, comments, criticisms, and suggestions are warmly welcomed!

–Allen

On Monday 9 March 2009 President Obama signed an executive order reversing the Bush administration’s ban on the use of Federal funding for embryonic stem cells for medical research (and presumably for any medical treatments that might eventually be developed as the result of that research). This policy change has raised a storm of controversy among right-to-life- advocates, and also among “intelligent design” supporters. This controversy has centered on the ethics of science, and whether scientists should be allowed to pursue their research wherever it leads.

Currently, most embryonic stem cells are derived from human egg cells that have been fertilized in vitro (that is, outside of the body of the egg-donor mother) as part of the process of in vitro fertilization (IVF) whereby childless couples can conceive of a baby using their own genetic material.

IVF clinics generally fertilize multiple donor eggs and then let them
divide by mitosis until the blastula stage is reached. During this process the inner cell mass is formed inside the blastula, from which embryonic stem cells are derived. The point to this process is not to produce the embryonic stem cells in the inner cell mass, but rather to produce viable blastulas, which can then be implanted in the uterus of the egg donor (or, in rare cases, a surrogate).

The way this process is carried out necessarily produces multiple unused blastula-stage embryos for every one that is implanted. These unused blastula-stage embryos are usually frozen in liquid nitrogen, in case the egg donor requires a repeat implantation.

Currently, there are almost half a million such blastula-stage embryos frozen in liquid nitrogen in IVF clinics in the United States, which leads to the first ethical question:

What becomes of the unused frozen embryos, and who decides?

Here is what generally happens:

Any embryos that you do not use in your first IVF attempt can be frozen for later use. This will save you money if you undergo IVF a second or third time. If you do not want your leftover embryos, you may donate them to another infertile couple, or you and your partner can ask the clinic to destroy the embryos. Both you and your partner must agree before the clinic will destroy or donate your embryos. [source]

So, should the “parents” (i.e. the egg and sperm donors) have the right to decide that their unused blastula-stage embryos be destroyed? Despite some political efforts to deny them this right, there is no legal jurisdiction in the U.S. in which this right has been abrogated (yet).

One way to solve this particular ethic dilemma is to “adopt” the frozen embryos by having them implanted in an “adoptive” mother. There is an organization that advocates this, Nightlight Christian Adoptions, and has arranged for some of these frozen embryos (which the organization calls “snowflakes”) to be “adopted” by implantation in “adoptive” mothers who are medically infertile (and married).

According to data at that website, the current number of successful “snowflake adoptions” is approximately 202 since the program was started in 1997. That works out to around 17 per year, or 0.0034% of the current half-million “snowflake backlog”. At that rate, all of the frozen embryos currently in cryogenic suspended animation will be “adopted” by the year 31421.

However, this grossly underestimates how long this backlog will persist, as it assumes that no new “snowflakes” are generated by new IVF procedures. Currently, the rate of production of new frozen blastula-stage embryos at IVF clinics in the US is approximately 18,000 per year. The current rate of “snowflake adoption” is approximately 20 per year, so unless IVF is permanently stopped, it is mathematically impossible for the current “snowflake backlog” to eventually be “adopted”.

One way to avoid the use of embryonic stem cells taken from frozen blastula-stage human embryos is to use adult stem cells instead. There are many different tissues in adult humans that qualify as pluripotent stem cells (that is, cells that can continue to divide by mitosis). Recent research has made it possible to “regress” adult stem cells almost to the embryonic stem cell stage, which raises the possibility of using adult stem cells instead of embryonic stem cells.

Personally, I strongly hope that adult stem cells can be used for all of the scientific and technical uses that most scientists originally thought only embryonic stem cells could be used for. However, this will then lead to two new, unforseen ethical dilemmas:

What will be done with the “snowflakes” that are currently frozen at IVF clinics, if they are not used for stem cell research and medical treatment?

and

What will be done with the adult stem cells that have been regressed to the embryonic stem cell stage, since these would then qualify genetically and developmentally as “snowflakes” themselves?

Clearly, one irony of the development of adult stem cell regression will be that the “snowflakes” now frozen in liquid nitrogen in all of those IVF labs will now almost certainly be disposed of (I suppose they defrost and incinerate them), rather than contributing to the advance of medical technology and human welfare.

The other irony, of course, is that by regressing adult stem cells to the embryonic stem cell stage, there would be many more “snowflakes”, rather than fewer, thereby necessitating the destruction of many more “potential human beings” than is currently the case.

There are two other solutions, both of which avoid the ethical dilemmas outlined above. One alternative would be:

To consider that neither embryonic stem cells nor adult stem cells are “human beings” until they are implanted into a mother and are born as human babies.

This, of course, would require defining “human life” as beginning at birth, rather than “conception” (regardless of where that “conception” took place).

Another alternative would be:

To consider that all stem cells are “human beings”, which would require that all stem cell research and treatment and all forms of in vitro fertilization be declared unethical, and presumably outlawed.

But this would also require that we outlaw all developmental research, because somewhere along the line some researcher somewhere might find out how to regress any human cell to the embryonic stem cell stage, and then simply scratching your head or drinking a cup of too-hot coffee would be equivalent to murder.

As always, comments, criticisms, and suggestions are warmly welcomed!

–Allen