Coyne vs. Shapiro

Jim Shapiro has been outlining his views on evolution over at the Huffington Post, including a posting entitled, What Is the Key to a Realistic Theory of Evolution?

Not surprisingly, Jerry Coyne does not like it and weighs in with a posting entitled, A colleague wrongfully disses modern evolutionary theory.

Let me focus on a key point of their disagreement.

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Failure to replicate

This is not good:

A former researcher at Amgen Inc has found that many basic studies on cancer — a high proportion of them from university labs — are unreliable, with grim consequences for producing new medicines in the future.

During a decade as head of global cancer research at Amgen, C. Glenn Begley identified 53 “landmark” publications — papers in top journals, from reputable labs — for his team to reproduce. Begley sought to double-check the findings before trying to build on them for drug development.

Result: 47 of the 53 could not be replicated. He described his findings in a commentary piece published on Wednesday in the journal Nature.

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Scientists Claim Brain Memory Code Cracked

Despite a century of research, memory encoding in the brain has remained mysterious. Neuronal synaptic connection strengths are involved, but synaptic components are short-lived while memories last lifetimes. This suggests synaptic information is encoded and hard-wired at a deeper, finer-grained molecular scale.

In an article in the March 8 issue of the journal PLoS Computational Biology, physicists Travis Craddock and Jack Tuszynski of the University of Alberta, and anesthesiologist Stuart Hameroff of the University of Arizona demonstrate a plausible mechanism for encoding synaptic memory in microtubules, major components of the structural cytoskeleton within neurons.

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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 genes originally believed to have evolved in animals. 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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Ten Signs of Intellectual Honesty

It’s been awhile since I reposted this….

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.

1. Do not overstate the power of your argument. One’s sense of conviction should be in proportion to the level of clear evidence assessable by most. If someone portrays their opponents as being either stupid or dishonest for disagreeing, intellectual dishonesty is probably in play. Intellectual honesty is most often associated with humility, not arrogance.

2. Show a willingness to publicly acknowledge that reasonable alternative viewpoints exist. The alternative views do not have to be treated as equally valid or powerful, but rarely is it the case that one and only one viewpoint has a complete monopoly on reason and evidence.

3. Be willing to publicly acknowledge and question one’s own assumptions and biases. All of us rely on assumptions when applying our world view to make sense of the data about the world. And all of us bring various biases to the table.

4. Be willing to publicly acknowledge where your argument is weak. Almost all arguments have weak spots, but those who are trying to sell an ideology will have great difficulty with this point and would rather obscure or downplay any weak points.

5. Be willing to publicly acknowledge when you are wrong. Those selling an ideology likewise have great difficulty admitting to being wrong, as this undercuts the rhetoric and image that is being sold. You get small points for admitting to being wrong on trivial matters and big points for admitting to being wrong on substantive points. You lose big points for failing to admit being wrong on something trivial.

6. Demonstrate consistency. A clear sign of intellectual dishonesty is when someone extensively relies on double standards. Typically, an excessively high standard is applied to the perceived opponent(s), while a very low standard is applied to the ideologues’ allies.

7. Address the argument instead of attacking the person making the argument. Ad hominem arguments are a clear sign of intellectual dishonesty. However, often times, the dishonesty is more subtle. For example, someone might make a token effort at debunking an argument and then turn significant attention to the person making the argument, relying on stereotypes, guilt-by-association, and innocent-sounding gotcha questions.

8. When addressing an argument, do not misrepresent it. A common tactic of the intellectually dishonest is to portray their opponent’s argument in straw man terms. In politics, this is called spin. Typically, such tactics eschew quoting the person in context, but instead rely heavily on out-of-context quotes, paraphrasing and impression. When addressing an argument, one should shows signs of having made a serious effort to first understand the argument and then accurately represent it in its strongest form.

9. Show a commitment to critical thinking. ‘Nuff said.

10. Be willing to publicly acknowledge when a point or criticism is good. If someone is unable or unwilling to admit when their opponent raises a good point or makes a good criticism, it demonstrates an unwillingness to participate in the give-and-take that characterizes an honest exchange.

While no one is perfect, and even those who strive for intellectual honesty can have a bad day, simply be on the look out for how many and how often these criteria apply to someone. In the arena of public discourse, it is not intelligence or knowledge that matters most – it is whether you can trust the intelligence or knowledge of another. After all, intelligence and knowledge can sometimes be the best tools of an intellectually dishonest approach.

– Mike Gene

A humbling reversal?

I have long noted that the case for non-teleological evolution was stronger in the past than it is in the present.  Consider this tiny example.

Below is a figure from Eukaryotic Evolution: Getting to the Root of the Problem (Simpson and Roger, Current Biology, Vol. 12, R691–R693, October 15, 2002).

The figure on the left is the eukaryotic phylogenetic tree from 1993 and before.  Simpson and Roger explain it as follows:

A decade ago, phylogenies based on small subunit ribosomal (r)RNA sequences provided an intuitively appealing evolutionary tree of eukaryotes. Complex eukaryotes, including animals, fungi, plants and most algae, emerged as a broad radiation usually called the ‘eukaryotic crown’ [1]. Below this ‘crown’, more bizarre, and generally simpler, organisms diverged in a ladder-like succession. The small subunit rRNA tree was ‘rooted’ with mitochondrion-lacking unicellular eukaryotes such as diplomonads, parabasalids and microsporidia forming the basal branches (Figure 1a).

Yes, this was intuitively appealing from a non-teleological, neo-darwinian viewpoint.

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Transposons from a non-telic perspective

Over at BioLogos, Dennis Venema provides the conventional view of transposons through a non-teleological prism.  Like many others, he thinks of transposons as parasites:

They are the perfect parasites: using their host to provide resources so they can replicate themselves, and with a “lifestyle” so simple that replication is essentially its only feature.


Despite their parasitic nature, sometimes the host species can exploit transposons as a source of genetic novelty.

Yet it is not really accurate to describe transposons as parasites.

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