Monthly Archives: January 2009

The Calcium Toolkit


As the sequence of the the unicellular choanoflagellate Monosiga brevicollis continues to be analyzed, it is now clear this “simple” creature is loaded with all kinds of animal genes. Today, let us consider the research of Xinjiang Ca, from Duke University Medical Center. Cai’s paper is entitled “Unicellular Ca2+ Signaling ‘Toolkit’ at the Origin of Metazoa” (Mol. Biol. Evol. 25(7):1357–1361. 2008).

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Front-loading Trees

If metazoan life was front-loaded, we would expect to find the components of metazoan machinery embedded in single-celled life forms. And this is indeed what science is finding. For example, on my old blog, I posted a series of essays showing that the components for epithelial tissue, the nervous system, and even the endocrine system, are found in various protozoa (I’ll repost these essays shortly).

But I have also noted that we would expect such front-loading to be coupled to terraforming, as a metazoan life form would be unlikely to exist on an otherwise sterile planet. Thus, it is encouraging to see that recent research provides some more evidence for front-loading that echoes both themes of deep homology and terraforming – a single-celled algae has been discovered to contain an important extracellular component previously seen only in land plants – lignin.

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It’s More Messy Than We Thought

Scientists recently took a closer look at Stanley Miller’s samples obtained from his famous spark-discharge experiments.

Because our instruments are much more sensitive than the tests Miller used, it was determined these experiments produced a wider variety of compounds than appreciated.

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The Rational Essence of Proteins and DNA

In my previous essay about proteins-as-design-material, I noted:

This all raises some interesting questions. For example, without proteins, and their manufacturing process, what becomes of the blind watchmaker? Without proteins, and the latent functions contained within, might not the blind watchmaker exist as the impotent, crippled, blind watchmaker with no one to notice its existence? If so, how much credit does the blind watchmaker really deserve?

The vast and immense Tree of Life is a protein-dependent output. Point to some evidence of evolution and I’ll point to the proteins that underlie it. Without proteins, would there be a Tree of Life 3.5 billion years after the RNA world took root? How do we know? If we believe so, would the Tree be as immense and vast as it is today? A life form composed of nucleic acids, carbohydrates, and lipids would suffice for the purposes of the blind watchmaker. But could the blind watchmaker turn this material into something that is analogous to an Ash tree filled with squirrels, beetles, and birds?

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New vs. Old Views of Evolution

If you haven’t seen it, be sure to check out this video. I especially enjoyed the comments from Sean Carroll (author of Endless Forms Most Beautiful):

So what this means is in some ways, some sense, evolution is a simpler process than we first thought. When you think about all of the diversity of forms out there, we first believed this would involve all sorts of novel creations, starting from scratch, again and again and again. We now understand that, no, that evolution works with packets of information and uses them in a new and different ways, and new and different combinations, without necessarily having to invent anything fundamentally new, but new combinations.

That’s a fairly radical change in the way we view evolution and this change has enhanced the plausibility of front-loading. What should catch your interest is that the old perspective of evolution was far more unfriendly to teleology than this new perspective.

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Naive Realism

An article in The Daily Gazette outlines Stanford psychologist Lee Ross’s theories about Naïve Realism. According to the article:

Naïve realism is the conviction that one sees the world as it is and that when people don’t see it in a similar way, it is they that do not see the world for what it is. Ross characterized naïve realism as “a dangerous but unavoidable conviction about perception and reality”. The danger of naïve realism is that while humans are good in recognizing that other people and their opinions have been shaped and influenced by their life experiences and particular dogmas, we are far less adept at recognizing the influence our own experiences and dogmas have on ourselves and opinions. We fail to recognize the bias in ourselves that we are so good in picking out in others.

Naïve realism is poison to any open-ended investigation. A good investigator must strive to remain open-minded and remain cognizant of his/her own biases. If a bias evolves into naïve realism, the investigator ceases to function as an investigator and becomes an apologist.

The Design Matrix helps to buffer against naïve realism in two ways.

First, since it recognizes and acknowledges the subjective dimension to a design inference and its assessment, TDM places great importance on intellectual honesty.

Second, the central metaphor of TDM is the Rabbit/Duck figure from Chapter 6. This is a truly unique way of approaching this issue and it amounts to an acknowledgment and understanding of both perspectives. For example, while I may chase the Rabbit, I am well aware that it also looks like a Duck. I see both. Those who come to the table with Naïve Realism will, more often than not, see only the Duck or the Rabbit. They truly believe they see the world as it is.

Intellectual Honesty in The Matrix

When I wrote The Design Matrix, I wanted to contribute something to the debate about intelligent design and evolution – an intellectually honest approach. So let me see how well the book holds up against the 10 signs of intellectual honesty:

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The Design Matrix Outline

I plan on making an effort to organize blog entries into an outline so readers can better connect the dots (a consilience of clues). I plan to periodically expand, update and repost this outline.

A. Detecting Design

1. Outline the common definitions of ‘subjective’ and ‘objective.’

2. Identify problems with common definitions and propose George Cooper’s definition of objective - that which can be measured by all parties who should obtain the same result given an appropriate range of accuracy.

3. Draw upon the wisdom of one the great biologists, Jacques Monod, to explain why science cannot determine whether or not life was designed.

4. Demonstrate how archeology and forensics fail to give us reason to think that science can determine whether or not life was designed.

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Similarities Between SETI and the Design Matrix

When it comes to inferring design, there are actually several points of significant similarity between SETI and the approach that I advocate in The Design Matrix

1. Neither SETI nor TDM expend much effort on precisely and rigorously defining “intelligence” before proceeding with the investigation. Instead, both extrapolate from our experience with the only known example of intelligent agency – us. This is because we have a wealth of information, both subjective and objective, about human designers.

2. Both SETI and TDM attempt to infer design without the luxury of having an independent base of knowledge about the proposed designers.

3. Both SETI and TDM eschew the purely negative approach, but can incorporate a negative approach as part of a larger investigative analysis without becoming a “gaps” argument. For example, when Seth Shostak argues, “Such a tone just doesn’t seem to be generated by natural astrophysical processes” and Steven Novella says, “finding an anomaly that cannot be explained by known natural processes,” they are appealing to discontinuities. But they are not claiming we should infer an intelligent cause based solely on this discontinuity/negative argument.

4. Both SETI and TDM bundle negative claims into an overall approach that includes a positive claim. For example, Novella writes, “The second, however, is positive – finding that the signal has markers of technological intelligence, as best as we can infer from our solitary self-example.” The positive claims draw upon analogy and what we know about design and designers. In The Design Matrix, the positive approach is split into three points of emphasis – Analogy with what is known to be designed, signs of Rational design, and hallmarks of Foresight.

5. Both SETI and TDM use what I call ‘inductive gradualism.’ That is, clues are gathered as part of an open-ended investigation as we attempt to probe whether the possibility of design is plausible and the plausibility of design is probable. As such, both SETI and TDM would require patience, an open mind, intellectual honesty, and a sensitivity to the clues.

6. Neither SETI not TDM amount to science, while there are many proponents of SETI and ID, respectively, who would disagree with this.

All of this tells me that the approach I advocate in TDM is indeed reasonable.

Of course, there are significant differences between SETI and TDM. I’ll consider these in the next installment.

10 Signs of Intellectual Honesty

When it comes to just about any topic, it seems as if the public discourse on the internet is dominated by rhetoric and propaganda. People are either selling products or ideology. In fact, just because someone may come across as calm and knowledgeable does not mean you should let your guard down and trust what they say. What you need to look for is a track record of intellectual honesty. Let me therefore propose 10 signs of intellectual honesty.

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