On irreconcilable differences between Darwin and God.

Character and Theology Aside, What About Denis Lamoureux's Science?

David Klinghoffer March 21, 2016 12:43 PM

As Denyse O'Leary points out, it's a good thing Stephen Meyer was thereon stage in Toronto, migraine attack or not. Otherwise, between atheist Lawrence Krauss and theistic evolutionist Denis Lamoureux, there would have been little to debate. Perhaps surprisingly, Lamoureux focused his attack on Meyer, even while proclaiming him his "brother in Christ" and flinging buttery approval at Krauss. Simple humanity, it seems, would have dictated turning your fire away from the stricken man and directing it at your shared opponent.

But I leave it to his fellow Christians to reflect on Dr. Lamoureux's character, and how little daylight there is between his "theistic" position and Krauss's atheism. What, though, about his science?

In defending Darwinism, Lamoureux's signal contribution drew on his expertise in teeth. Evolving them was a snap -- "Teeth emerged. Very easy to do." Paleontologist Günter Bechly, a pretty impressive scientist, begs to differ, on that as well as other points raised by Lamoureux. He blogs about the "Lamoureux delusion." First on the question of dental evolution:

Lamoureux elaborated on the origin of teeth from placoid scales on the jaws of Paleozoic acanthodian "sharks". However, his own diagram showed that these placoid scales already included all crucial morphological features of teeth (upper enamel layer, lower dentine layer, pulp cavity, bony base). That dermal denticle scales on jaws gradually grew larger to form teeth is not a convincing example of macroevolution, but rather just quantitative change through microevolution that is not even denied by Young Earth Creationists. At best, his example is evidence for common descent with modification, which is fully compatible with Intelligent Design and thus cannot be used against it. Finally, the example has no bearing at all on the crucial question, if an unguided Neodarwinian process can explain the pattern of morphological change over time, and therefore it is impotent as an argument against Intelligent Design anyway.

On Lamoureux and the "oldest bilaterian":

To refute Stephen Meyer's claims in his book "Darwin's Doubt", Lamoureux presented the discovery of alleged 585 million year old traces of early bilaterian animals from the Ediacaran period. This evidence is based on a Science publication byPecoits et al. (2012). However, Lamoureux forgot to mention that the dating and identification of these traces is highly disputed (see here and here). Actually, the most recent publication on this issue by Mángano & Buatois (2014) clearly states that "With respect to the Ediacaran, we agree with more conservative estimations that the oldest bilaterian trace fossils are dated to approximately 560 Ma ... The oldest subdivision (Avalon; 575-560 Ma) does not contain undisputed bilaterian trace fossils, and therefore has not been considered ... An earlier appearance of bilaterian trails (585 Ma) has been recently suggested. However, the age of the trace-fossil-bearing strata is highly contended, probably being Late Palaeozoic".

It is especially noteworthy that large unicellular organisms (protists) can produce traces on the sea floor that are remarkably similar to those of bilaterian animals, as Matz et al. (2008) showed in a study titled "Giant deep-sea protist produces bilaterian-like traces".

On nylonase:

Lamoureux mentioned the discovery of Nylon-eating bacteria as empirical proof that evolution can create new complex specified information and new proteins (nylonase enzyme) within only 40 years of time. This is actually an "old hat" in the creation vs evolution debate (see Wikipedia), and it sounds impressive only when one ignores two facts:

1. Dembski (2001) established in his book "No Free Lunch" a value 500 Bits as complexity threshold for Complex Specified Information (CSI), which could not originate by natural processes given the probabilistic resources of our universe. It has not been established that the new information in nylonase matches this threshold and thus represents CSI at all (see here).
2. Newer research by Negoro et al. (2007) has shown that the nylonase enzyme did not evolve by gene duplication and frameshift mutation as originally assumed, but arose from a pre-existing carboxyesterase enzyme, which already had some capacity to degrade nylon oligomers. In other words: Nylonase is NOT new information (also see here)!

On the "God of the gaps" objection, Bechly agrees that "explaining lightning and thunder with Thor's activity" would be "a God of the Gaps argument." But ID is different, obviously:

As Intelligent Design theorist Stephen C. Meyer explained in the same debate and in his books "Signature in the Cell" and "Darwin's Doubt", Intelligent Design makes an inference to the best explanation, not based on an argument from ignorance (what we do NOT know), but based on what we DO know about causes now in operation that could bring about the effect in question.

These are fighting words:

Indeed it is Theistic Evolution which is a redundant and dispensable concept (see this Forbes article), because it is either Neodarwinism in a cheap tuxedo (which it usually is), or it is a cowardly euphemism for Intelligent Design. In either case it is not a genuine alternative to Neodarwinism or Intelligent Design.

"Neo-Darwinism in a cheap tuxedo" -- I like that. Or maybe in rented clerical attire.

The appearance of evenhandedness?

Larry Moran -- Voice of Reason

Ann Gauger March 21, 2016 1:58 PM

We weren't the only ones to notice Krauss's "shenanigans" duringSaturday's debate with Meyer and Lamoureux. Over at his blogSandwalk, biochemist Larry Moran of the University of Toronto (where the event took place) posted a straightforward commentary, without innuendo or name-calling (aside from his usual label of "intelligent design creationists").

The main point that he picked up from Stephen Meyer's presentation was the argument that ID predicted the functionality of most of the genome, rather than its being mostly junk. ID proponent Richard Sternberg made this claim in the 1990s, and it is being confirmed by ongoing research and the ENCODE project. Moran argues that ENCODE doesn't demonstrate what ID proponents claim, and that the genome still is full of junk. But that's an argument that time and more research will answer.

The really interesting thing is what happened in the comments section after the post. He acknowledged that some ID proponents do science in good faith (in contrast to Krauss's repeated assertions during the debate):

I believe that there are ID proponents who are attempting to perform science in good faith.

Let's not quibble over when ID proponents made a prediction and whether it counts as a true predication [sic]. Right now, they are staking the reputation of ID on the claim (= prediction) that most of our genome is functional.

We'll see what happens when they realize the truth.

Then further on, in response to an attack on ID by a poster he says,

Bill says,

But the point is moot. ID is not a scientific endeavor. Never has been. It's a political movement with a social agenda to inject religion into American public schools. Simple as that.

The debate took place in Canada where we allow the teaching of religion in public schools. None of us give a damn about the American Constitution. We're interest[ed] in knowing whether the science is valid or not.

If the Intelligent Design proponents have legitimate complaints about evolution and if they have good scientific arguments in favor of design then those ideas should be taught in Canadian schools in spite of what some judge in Pennsylvania said ten years ago.

Lawrence Krauss tried to show that ID was not science but he did a horrible job. Meyer countered by presenting a lot of science forcing Krauss to deal with the very science that he said ID doesn't do!

Bill, you are being dangerously naive if you think you can simply dismiss the ID movement because it's not science (according to your definition). The general public doesn't care. All they see is serious attacks on evolution that look a lot like science.

Yes, ID is a movement and so are the desires to do something about climate change or GMO's. There are lots of "movements" with social and political agenda[s]. Many of them deal with science in one way [or] another. It's the role of scientists to evaluate the scientific arguments in spite of the agenda. We have to show that the goal of the movement is either compatible or incompatible with the scientific facts.

Yes. That's the level at which the debate should be held.

It doesn't mean that Moran agrees with us. He's just being fair. He even granted Meyer some points in the debate, before expressing his own view:

During the debate, Stephen Meyer emphasized [the] random nature of evolution and its inability -- according to him -- to come up with new protein folds and new information in a reasonable amount of time.

Krauss misunderstood the argument, which was based on the frequency of mutations, and tried to dismiss it by pointing out that evolution is not random -- it's directed and guided by natural selection.

Meyer corrected him by pointing out that the issue was the probability of mutations and not the probability of fixation once the mutation occurred. (This was when he was struggling with a migraine so he didn't do as good a job as he could have.)

Krauss stumbled on for a bit emphasizing natural selection and the fact that evolution is not random.

That was embarrassing. I think Krauss gets most of his information about evolution from Richard Dawkins so he (Krauss) probably doesn't know about random genetic drift or historical contingency or any of the other features of the history of life that make it "random" (in the colloquial sense).

I suspect that Krauss still holds on to the Dawkins view that life has the appearance of design. Truth is, in the big picture, life really doesn't have the appearance of design. Certainly our genome doesn't look designed and my back was not designed for walking upright as it let's me know every morning when I get out of bed.

Designed or not, Professor Larry Moran has distinguished himself as someone even-handed in his assessment of this debate. Thanks for the voice of reason, Dr. Moran.

The salmon vs. Darwin

Another Fine-Tuned Mechanism Gets Salmon Home

Evolution News & Views March

What is carbonic anhydrase and why does it matter? The presence of this enzyme in salmon hearts points to another case of intelligent design in these remarkable fish that were depicted in Illustra Media's film Living Waters. News via the Journal of Experimental Biology explains the challenge salmon face swimming upstream:

Fish plumbing is contrary. As the heart is the last organ that blood passes through before it returns to the gills, and with little direct blood supply to the ceaselessly contracting muscle, there are occasions when it could be on the verge of failure. 'We know this can happen under certain conditions like exhaustive exercise in combination with hypoxia or elevated water temperature', says Sarah Alderman from the University of Guelph, Canada. Added to the challenge of keeping the heart supplied with oxygen, Alderman explains that the haemoglobin that carries oxygen in fish blood is finely tuned to blood pH: the more acidic the red blood cells, the less able haemoglobin is to carry oxygen, which could prevent the red blood cells of exercising fish from picking up oxygen at the gills if they didn't have an effective pump to remove acid from the cells and restore the pH balance. [Emphasis added.]

Here we see a double challenge the salmon faces. It has to avoid excess acid so that the hemoglobin can carry oxygen, and it has to get the oxygen all the way from the gills through its entire body to the heart. Here's where carbonic anhydrase comes to the rescue:

But Alderman and her colleagues, Till Harter, Tony Farrell and Colin Brauner from the University of British Columbia, Canada, also knew that fish can take advantage of a sudden drop in red blood cell pH to release oxygen rapidly at tissues -- such as red muscle and the retina -- when required urgently. An enzyme called carbonic anhydrase -- which combines CO2 and water to produce bicarbonate and acidic protons, and vice versa -- lies at the heart of this mechanism. Normally there is no carbonic anhydrase in blood plasma; however, the enzyme has been found in salmon red muscle capillaries, where it facilitates the reaction of protons -- that have been extruded from the red blood cell -- with bicarbonate to produce CO2, which then diffuses back into the red blood cell. The CO2 is then converted back into bicarbonate and protons in the blood cell, causing the pH to plummet and release a burst of O2 from the haemoglobin. Could salmon take advantage of this mechanism to boost oxygen supplies to the heart when the animals are working full out? Possibly, but only if carbonic anhydrase was accessible to blood passing through the heart.What is carbonic anhydrase and why does it matter? The presence of this enzyme in salmon hearts points to another case of intelligent design in these remarkable fish that were depicted in Illustra Media's film Living Waters. News via the Journal of Experimental Biology explains the challenge salmon face swimming upstream:

Fish plumbing is contrary. As the heart is the last organ that blood passes through before it returns to the gills, and with little direct blood supply to the ceaselessly contracting muscle, there are occasions when it could be on the verge of failure. 'We know this can happen under certain conditions like exhaustive exercise in combination with hypoxia or elevated water temperature', says Sarah Alderman from the University of Guelph, Canada. Added to the challenge of keeping the heart supplied with oxygen, Alderman explains that the haemoglobin that carries oxygen in fish blood is finely tuned to blood pH: the more acidic the red blood cells, the less able haemoglobin is to carry oxygen, which could prevent the red blood cells of exercising fish from picking up oxygen at the gills if they didn't have an effective pump to remove acid from the cells and restore the pH balance. [Emphasis added.]

Here we see a double challenge the salmon faces. It has to avoid excess acid so that the hemoglobin can carry oxygen, and it has to get the oxygen all the way from the gills through its entire body to the heart. Here's where carbonic anhydrase comes to the rescue:

But Alderman and her colleagues, Till Harter, Tony Farrell and Colin Brauner from the University of British Columbia, Canada, also knew that fish can take advantage of a sudden drop in red blood cell pH to release oxygen rapidly at tissues -- such as red muscle and the retina -- when required urgently. An enzyme called carbonic anhydrase -- which combines CO2 and water to produce bicarbonate and acidic protons, and vice versa -- lies at the heart of this mechanism. Normally there is no carbonic anhydrase in blood plasma; however, the enzyme has been found in salmon red muscle capillaries, where it facilitates the reaction of protons -- that have been extruded from the red blood cell -- with bicarbonate to produce CO2, which then diffuses back into the red blood cell. The CO2 is then converted back into bicarbonate and protons in the blood cell, causing the pH to plummet and release a burst of O2 from the haemoglobin. Could salmon take advantage of this mechanism to boost oxygen supplies to the heart when the animals are working full out? Possibly, but only if carbonic anhydrase was accessible to blood passing through the heart.

Well, what do you know! That's what Alderman's team found: the enzyme is present on the surface of the heart chambers. Using the heart itself as their "reaction vessel," they were able to see the pH plummet as the enzymes went into gear. 

Working closely together, the duo painstakingly developed a technique where they could measure the pH in the beating heart with pH probes that were thinner than a human hair. Eventually, the duo's persistence paid off and the pH in the heart plummeted as they fed CO2 into the pulsating chambers. And when they added a carbonic anhydrase inhibitor (produced by Claudia Supuran) to the fluid, the pH fall slowed dramatically. Carbonic anhydrase was responsible for the drop in pH.

The Protein Data Bank 101 website shows pictures of this enzyme and describes its mode of action. 

An enzyme present in red blood cells, carbonic anhydrase, aids in the conversion of carbon dioxide to carbonic acid and bicarbonate ions. When red blood cells reach the lungs, the same enzyme helps to convert the bicarbonate ions back to carbon dioxide, which we breathe out. Although these reactions can occur even without the enzyme, carbonic anhydrase can increase the rate of these conversions up to a million fold.

There's an evolutionary conundrum about this enzyme: functional equivalence without sequence similarity:

This ancient enzyme has three distinct classes (called alpha, beta and gamma carbonic anhydrase). Members of these different classes share very little sequence or structural similarity, yet they all perform the same function and require a zinc ion at the active site. Carbonic anhydrase from mammals belong to the alpha class, the plant enzymes belong to the beta class, while the enzyme from methane-producing bacteria that grow in hot springs forms the gamma class. Thus it is apparent that these enzyme classes have evolved independently to create a similar enzyme active site.

Further complicating the picture, there are different forms of the enzymes depending on the tissue or cellular compartment they are located in. These allow fine tuning of the enzyme's activity: "Thus isozymes found in some muscle fibers have low enzyme activity compared to that secreted by salivary glands," in the case of mammals.Carbonic anhydrase (CA) was the first enzyme found to contain zinc, abiochemistry textbook says; now, hundreds are known. Zinc and other metals are often essential for function in metalloenzymes. The PDB-101 article explains,

Zinc is the key to this enzyme reaction. The water bound to the zinc ion is actually broken down to a proton and hydroxyl ion. Since zinc is a positively charged ion, it stabilizes the negatively charged hydroxyl ion so that it is ready to attack the carbon dioxide.

It's not surprising that this enzyme is present in the salmon, since it exists in all three domains of life. What's amazing is that the salmon's heart is studded with these enzymes that are "at the ready" when the large fish is fighting with all its might to leap above cascades and waterfalls, facing daunting challenges without the benefit of food. (Living Waters says, "The sockeye are so focused on their objective that after leaving the ocean, they do not eat again.")

If the pH dropped too early as the blood travels through the salmon's body, it would be less able to carry its precious oxygen cargo. But right when it is needed during that Olympic high jump over a waterfall or away from a hungry bear, the fish uses its CA enzymes in its heart to drop the pH and release the oxygen it needs. The spent blood then travels to the gills to load up with more oxygen. In the original paper in the Journal of Experimental Biology, the authors summarize what they found:

Combined, these results support our hypothesis of thepresence of an enhanced oxygen delivery system in the lumen of a salmonid heart, which could help support oxygen delivery when the oxygen content of venous blood becomes greatly reduced, such as after burst exercise and duringenvironmental hypoxia.

How many independent systems do we see at work in the remarkable migration of the salmon? The fish has a built-in map of its destination. It has the ability to memorize waypoints by smell. It can navigate by the earth's magnetic field. It has a sixth sense, the lateral line. It can distinguish odors by parts per trillion. Each of its body systems contain thousands of molecular machines like carbonic anhydrase that are located just where they need to be, doing what they need to do to support the whole organism.

If any one of these systems is a testament to intelligent design, how much more the composite? The only fish story here is the notion that all this came together by unguided natural processes -- sheer dumb luck.