Homology explains phylogeny(except when it doesn't)

Theory of Convergent Evolution Analyzed

Evolution News & Views 

The knifefish, rather than having several fins like a trout, has one long "ribbon fin" that undulates along the length of its body. Studies of its motion reveal that it uses the optimal wavelength to get the most forward thrust, stability, and maneuverability out of its investment of energy. But the knifefish is not alone: the same optimal design can be found in cuttlefish (cephalopods), rays (cartilaginous fish), certain flatworms, and other bony fish that are evolutionarily unrelated. In fact -- if evolution by natural selection is assumed to be the cause -- this design emerged independently at least eight times. To the Darwinian, it's another remarkable case of "convergent evolution."

A paper in PLOS Biology investigates this phenomenon and tries to explain it. The five authors, primarily from Northwestern University, used a robotic knifefish to nail down the physical factors related to optimal swimming design: the length of the fin's undulation and the mean amplitude. Dividing the one by the other yields what they call the Optimal Specific Wavelength (OSW). Then they measured the OSW on 22 live swimmers, such as cuttlefish and rays, to see how they rated. They found that the values "converge to a narrow range" around 20, even though the animals belong to eight separate groups whose presumed ancestors did not possess this kind of propulsion. Robin Meadows says in a companion piece likewise in PLOS Biology:

Many OSW swimmers have no known ancestor that swam with median/paired fins, and the 22 species in this analysis belong toeight clades (groups of organisms stemming from a common ancestor). This suggests that the OSW evolved independently at least eight times. 

Casey Luskin has argued that Darwinians appeal to convergence in order to have it both ways: basically, "biological similarity implies common ancestry, except when it doesn't." The authors of this new paper do not respond to that charge specifically, but they go further than most Darwinians by not just asserting convergence occurred, but by offering evolutionary mechanisms that might produce it. They begin with broad philosophical questions:

How would life look if it evolved again on Earth, or for that matter, on any other habitable planet? The question of the role of chance versus necessity in evolution is a foundational issue in biology. Gould gave us the metaphor of the "tape of life" for the evolution of life and argued that if it were somehow rewound and started again, life would have taken a very different course. Conway Morris has argued that, on the contrary, the laws of physics limit the number of good solutions that are within reach of evolution, and that therefore we should expect life to take a similar course upon rewinding. Examples of convergent evolution, such as wings on insects, birds, and mammals, are considered supporting evidence for this hypothesis.But our understanding of convergent evolution, as reflecting the dominance of natural selection plus variation over factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, and other stochastic processes, is held back by a lack of quantitative arguments. Such arguments would expose the links from physical principles to the biological phenomena and help us understand where evolution is likely to converge to the same result or diverge to a wide variety of solutions.

Here, we present just such arguments for a phenomenon that unifies a vast diversity of swimming organisms, from invertebrates, like cuttlefish, to vertebrates, like cartilaginous and bony fish. Unlike the case of the convergently evolved wing, a morphological feature, here the evolved feature is a pattern of movement that occurs across a morphologically diverse set of moving appendages on aquatic animals.

We see at once that the implications go far beyond the knifefish's OSW. Evolutionary theory itself is at stake: Is it truly contingent, or somehow directed? Their argument hinges on the ability of the environment (e.g., the properties of water) to direct natural selection so that it rewards, with higher fitness, the animals that hit the optimum. If the OSW is on a peak of the fitness landscape, natural selection will drive an animal up the peak, no matter its ancestry, because it will outcompete the others. That's how separately evolving animals will end up (converge) on the same fitness peak.

What is the mechanism for macroevolutionary repeatability? In the language of the calculus of variations, these examples of convergent evolution -- if correctly identified as such -- imply that there is agradient in the fitness landscape toward some optimum with respect to trait in question, and this gradient is large enough to overcome competing factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, cases where optimality in one trait results in suboptimality in another trait ... and approximations of the trait which provide local but not global optimality. With a sufficiently steep gradient in fitness in place and evolutionary dynamics capable of achieving near-optimal solutions, it is only a matter of time before the mechanism of selection with variation can arrive at the optimum. As the derivative of the trait with respect to fitness is stabilizing,departures from the optimum would be self-correcting over evolutionary time.

In fulfillment of the promise of quantifying their argument, they measure the loss in force for wavelengths that deviate significantly from the OSW. "The effect of any decline in propulsive force -- even less than one percent -- from what it is at the OSW is amplified over the vast number of undulations an animal may make in its life," they argue. What animal would want to compete with less than the best?

Unfortunately, undulating fins are not the best. Tuna are the fastest swimmers in the ocean, but they rely on their caudal fins to thrust their bodies forward. So we have a conundrum; "The question is therefore why the slower forms of swimming exhibited by median/paired fin animals would emerge and thrivedespite the prevalence of body/caudal fin swimming in ancestral species." Why would evolution switch from the Ferrari to the Volkswagen?

The authors are ready with auxiliary hypotheses:

A similar question has arisen in simulation studies that show that alight-sensitive patch of skin can evolve through several intermediate forms into an advanced camera-type lens eye in only a few hundred thousand years -- why, then, are there so many existing animals with intermediate forms of eyes? Nilsson and Pelger's answer is that camera-type lens eyes are only the best solution for certain animal -- ecosystem combinations. Our answer is similar: body/caudal fin swimming makes little sense in isolation. It is only within particular ecological contexts that some types of animals are able to survive better with this type of swimming than with alternative approaches.

In particular, median/paired fin swimming appears to be a low speed, low cost of transport specialization. The lower amplitudes of fin movement that are possible in median/paired fin swimmers, compared to the very high amplitudes possible when the high power axial musculature is used in body/caudal fin swimmers, is thereforean advantage instead of a liability due to the lower energetic cost of transport of median/paired fin swimming. The fact that median/paired fin swimming is used at lower speeds should not be confused, however, with the concept of maximizing speed by swimming at the OSW. Even when swimming at lower speeds (or whatever speed for that matter, which is determined by frequency and amplitude), for a given set of parameters (amplitude of undulations, frequency, fin height, and fin shape), if an animal swims with elongated median/paired fins, then its speed can be maximizedfor that set of parameters by swimming at the OSW.

Our regular readers will jump at that lateral pass to Nilsson and Pelger. Their claim about the evolution of camera eyes was thoroughly trounced by David Berlinski almost a decade ago in these pages. It's an example of how scientists can continue to trust flawed arguments for years -- decades, sometimes -- without considering (or even knowing about) the counter-arguments.

Aside from that, the authors make a point: You can't just look at a fin in isolation. You need to consider the ecological niche of the animal. They point to members of the group Gymnotiformes, electric fish who use their ribbon fins in low-oxygen murky waters, that swim mostly at night where high speed is not advantageous.

Given these constraints, the elongated fins that are universally present within the more than 150 species comprising Gymnotiformesmay be favored, but clearly a tremendous amount of work would need to be done to assess the relative importance of all of these factors in giving rise to this one group of median/paired fin swimmers.

While the existence of body/caudal fin swimmers and the existence of median/paired fin swimmers may or may not be subject to robust repeatability, what is clear is that if median/paired fin swimming with elongated fins and semirigid trunks emerges -- as it has independently on multiple occasions according to Fig 1 -- it is very probable that the specific trait of swimming at the OSW will also emerge.

This is a very different claim, much reduced from the original one. No longer are they asserting that the environment will force different swimmers up the same fitness peak, because clearly it didn't for the tuna. Now we have the more modest claim that "if" a ribbon fin "emerges," then natural selection will push it toward the OSW. But where is their scientific law of emergence? What about the ocean environment can cause that? And we see they just admitted that their hypothesis "may or may not be subject to robust repeatability."

Another complication is that some of the undulating-fin fish can switch to high-speed caudal-fin swimming when needed, as when under attack from predators or when zooming in on prey. Why would natural selection provide both methods of propulsion? The fitness landscape just got more complicated; the animal has to climb multiple fitness peaks to survive. (We might point out, in passing, that according to evolutionists, electric organs are examples of convergence, too, having evolved six times independently according to a report last year from the University of Wisconsin posted at NewsWise.)

Notice, also, that while the ecological hypothesis seems to work for the Gymnotiformes, it doesn't for the others. Rays and cuttlefish, for instance, use their undulating fins in the open sea or coastal shallows during the daytime. The authors have not shown that their auxiliary hypotheses rescue convergent evolution, nor have they identified any evolutionary mechanism to account for fast swimmers with caudal fins swimming right alongside slow swimmers with undulating fins in the exact same watery environment. Every proposal has exceptions; where is that quantitative argument, exactly?

Thus, we can only speculate that the 7.5% decline in force occurring over the observed variation in SW is not large enough to overcomethe many causes of suboptimality listed above, whereas the 25% decline we find beyond this range is large enough to cause selection pressure toward the OSW. Additional research is needed to establish whether this hypothesis is true.

We thus circle back to Casey Luskin's challenge: Common ancestry explains traits, except when it doesn't.

For these reasons, we cannot take Robin Meadows's praise of this paper seriously:

This elegant work reveals that a physical problem -- how to get from here to there -- can be optimized by a wondrous diversity of biological solutions. Moreover, these findings strengthen the case thatmechanical optimization can drive evolution, contributing to the longstanding debate over the evolutionary roles of randomness versus physical constraints that limit the solutions that are feasible in living creatures. As the researchers point out, quantifying physical properties that underlie biological phenomena could help us recognize when an optimal mechanical solution is likely to drive convergent evolution.

Ockham is tapping his foot by the door.e knifefish, rather than having several fins like a trout, has one long "ribbon fin" that undulates along the length of its body. Studies of its motion reveal that it uses the optimal wavelength to get the most forward thrust, stability, and maneuverability out of its investment of energy. But the knifefish is not alone: the same optimal design can be found in cuttlefish (cephalopods), rays (cartilaginous fish), certain flatworms, and other bony fish that are evolutionarily unrelated. In fact -- if evolution by natural selection is assumed to be the cause -- this design emerged independently at least eight times. To the Darwinian, it's another remarkable case of "convergent evolution."

A paper in PLOS Biology investigates this phenomenon and tries to explain it. The five authors, primarily from Northwestern University, used a robotic knifefish to nail down the physical factors related to optimal swimming design: the length of the fin's undulation and the mean amplitude. Dividing the one by the other yields what they call the Optimal Specific Wavelength (OSW). Then they measured the OSW on 22 live swimmers, such as cuttlefish and rays, to see how they rated. They found that the values "converge to a narrow range" around 20, even though the animals belong to eight separate groups whose presumed ancestors did not possess this kind of propulsion. Robin Meadows says in a companion piece likewise in PLOS Biology:

Many OSW swimmers have no known ancestor that swam with median/paired fins, and the 22 species in this analysis belong toeight clades (groups of organisms stemming from a common ancestor). This suggests that the OSW evolved independently at least eight times. [Emphasis added.]

Casey Luskin has argued that Darwinians appeal to convergence in order to have it both ways: basically, "biological similarity implies common ancestry, except when it doesn't." The authors of this new paper do not respond to that charge specifically, but they go further than most Darwinians by not just asserting convergence occurred, but by offering evolutionary mechanisms that might produce it. They begin with broad philosophical questions:

How would life look if it evolved again on Earth, or for that matter, on any other habitable planet? The question of the role of chance versus necessity in evolution is a foundational issue in biology. Gould gave us the metaphor of the "tape of life" for the evolution of life and argued that if it were somehow rewound and started again, life would have taken a very different course. Conway Morris has argued that, on the contrary, the laws of physics limit the number of good solutions that are within reach of evolution, and that therefore we should expect life to take a similar course upon rewinding. Examples of convergent evolution, such as wings on insects, birds, and mammals, are considered supporting evidence for this hypothesis.But our understanding of convergent evolution, as reflecting the dominance of natural selection plus variation over factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, and other stochastic processes, is held back by a lack of quantitative arguments. Such arguments would expose the links from physical principles to the biological phenomena and help us understand where evolution is likely to converge to the same result or diverge to a wide variety of solutions.

Here, we present just such arguments for a phenomenon that unifies a vast diversity of swimming organisms, from invertebrates, like cuttlefish, to vertebrates, like cartilaginous and bony fish. Unlike the case of the convergently evolved wing, a morphological feature, here the evolved feature is a pattern of movement that occurs across a morphologically diverse set of moving appendages on aquatic animals.

We see at once that the implications go far beyond the knifefish's OSW. Evolutionary theory itself is at stake: Is it truly contingent, or somehow directed? Their argument hinges on the ability of the environment (e.g., the properties of water) to direct natural selection so that it rewards, with higher fitness, the animals that hit the optimum. If the OSW is on a peak of the fitness landscape, natural selection will drive an animal up the peak, no matter its ancestry, because it will outcompete the others. That's how separately evolving animals will end up (converge) on the same fitness peak.

What is the mechanism for macroevolutionary repeatability? In the language of the calculus of variations, these examples of convergent evolution -- if correctly identified as such -- imply that there is agradient in the fitness landscape toward some optimum with respect to trait in question, and this gradient is large enough to overcome competing factors such as developmental constraints, pleiotropy, phylogenetic inertia, genetic drift, cases where optimality in one trait results in suboptimality in another trait ... and approximations of the trait which provide local but not global optimality. With a sufficiently steep gradient in fitness in place and evolutionary dynamics capable of achieving near-optimal solutions, it is only a matter of time before the mechanism of selection with variation can arrive at the optimum. As the derivative of the trait with respect to fitness is stabilizing,departures from the optimum would be self-correcting over evolutionary time.

In fulfillment of the promise of quantifying their argument, they measure the loss in force for wavelengths that deviate significantly from the OSW. "The effect of any decline in propulsive force -- even less than one percent -- from what it is at the OSW is amplified over the vast number of undulations an animal may make in its life," they argue. What animal would want to compete with less than the best?

Unfortunately, undulating fins are not the best. Tuna are the fastest swimmers in the ocean, but they rely on their caudal fins to thrust their bodies forward. So we have a conundrum; "The question is therefore why the slower forms of swimming exhibited by median/paired fin animals would emerge and thrivedespite the prevalence of body/caudal fin swimming in ancestral species." Why would evolution switch from the Ferrari to the Volkswagen?

The authors are ready with auxiliary hypotheses:

A similar question has arisen in simulation studies that show that alight-sensitive patch of skin can evolve through several intermediate forms into an advanced camera-type lens eye in only a few hundred thousand years -- why, then, are there so many existing animals with intermediate forms of eyes? Nilsson and Pelger's answer is that camera-type lens eyes are only the best solution for certain animal -- ecosystem combinations. Our answer is similar: body/caudal fin swimming makes little sense in isolation. It is only within particular ecological contexts that some types of animals are able to survive better with this type of swimming than with alternative approaches.

In particular, median/paired fin swimming appears to be a low speed, low cost of transport specialization. The lower amplitudes of fin movement that are possible in median/paired fin swimmers, compared to the very high amplitudes possible when the high power axial musculature is used in body/caudal fin swimmers, is thereforean advantage instead of a liability due to the lower energetic cost of transport of median/paired fin swimming. The fact that median/paired fin swimming is used at lower speeds should not be confused, however, with the concept of maximizing speed by swimming at the OSW. Even when swimming at lower speeds (or whatever speed for that matter, which is determined by frequency and amplitude), for a given set of parameters (amplitude of undulations, frequency, fin height, and fin shape), if an animal swims with elongated median/paired fins, then its speed can be maximizedfor that set of parameters by swimming at the OSW.

Our regular readers will jump at that lateral pass to Nilsson and Pelger. Their claim about the evolution of camera eyes was thoroughly trounced by David Berlinski almost a decade ago in these pages. It's an example of how scientists can continue to trust flawed arguments for years -- decades, sometimes -- without considering (or even knowing about) the counter-arguments.

Aside from that, the authors make a point: You can't just look at a fin in isolation. You need to consider the ecological niche of the animal. They point to members of the group Gymnotiformes, electric fish who use their ribbon fins in low-oxygen murky waters, that swim mostly at night where high speed is not advantageous.

Given these constraints, the elongated fins that are universally present within the more than 150 species comprising Gymnotiformesmay be favored, but clearly a tremendous amount of work would need to be done to assess the relative importance of all of these factors in giving rise to this one group of median/paired fin swimmers.

While the existence of body/caudal fin swimmers and the existence of median/paired fin swimmers may or may not be subject to robust repeatability, what is clear is that if median/paired fin swimming with elongated fins and semirigid trunks emerges -- as it has independently on multiple occasions according to Fig 1 -- it is very probable that the specific trait of swimming at the OSW will also emerge.

This is a very different claim, much reduced from the original one. No longer are they asserting that the environment will force different swimmers up the same fitness peak, because clearly it didn't for the tuna. Now we have the more modest claim that "if" a ribbon fin "emerges," then natural selection will push it toward the OSW. But where is their scientific law of emergence? What about the ocean environment can cause that? And we see they just admitted that their hypothesis "may or may not be subject to robust repeatability."

Another complication is that some of the undulating-fin fish can switch to high-speed caudal-fin swimming when needed, as when under attack from predators or when zooming in on prey. Why would natural selection provide both methods of propulsion? The fitness landscape just got more complicated; the animal has to climb multiple fitness peaks to survive. (We might point out, in passing, that according to evolutionists, electric organs are examples of convergence, too, having evolved six times independently according to a report last year from the University of Wisconsin posted at NewsWise.)

Notice, also, that while the ecological hypothesis seems to work for the Gymnotiformes, it doesn't for the others. Rays and cuttlefish, for instance, use their undulating fins in the open sea or coastal shallows during the daytime. The authors have not shown that their auxiliary hypotheses rescue convergent evolution, nor have they identified any evolutionary mechanism to account for fast swimmers with caudal fins swimming right alongside slow swimmers with undulating fins in the exact same watery environment. Every proposal has exceptions; where is that quantitative argument, exactly?

Thus, we can only speculate that the 7.5% decline in force occurring over the observed variation in SW is not large enough to overcomethe many causes of suboptimality listed above, whereas the 25% decline we find beyond this range is large enough to cause selection pressure toward the OSW. Additional research is needed to establish whether this hypothesis is true.

We thus circle back to Casey Luskin's challenge: Common ancestry explains traits, except when it doesn't.

For these reasons, we cannot take Robin Meadows's praise of this paper seriously:

This elegant work reveals that a physical problem -- how to get from here to there -- can be optimized by a wondrous diversity of biological solutions. Moreover, these findings strengthen the case thatmechanical optimization can drive evolution, contributing to the longstanding debate over the evolutionary roles of randomness versus physical constraints that limit the solutions that are feasible in living creatures. As the researchers point out, quantifying physical properties that underlie biological phenomena could help us recognize when an optimal mechanical solution is likely to drive convergent evolution.

Ockham is tapping his foot by the door.

On being argumentative in lieu of making an argument.

Integrity in Science — A Facebook Dialogue
Ann Gauger

Editor’s note: Our biologist colleague Ann Gauger had the following interaction on Facebook yesterday. Sadly typical, it speaks for itself.

Questioner: Has anyone in the Discovery Institute thought of doing any real experiments?

Ann Gauger: Read our papers. Plenty of real experiments there.

Q: Where, Ann Gauger?

Ann: [LINK]

Q: “Peer review” means different things in science and in intelligent design. Yet more deception.

Q: I don’t see any evidence of any science being done.

Another FB correspondent chimes in:

[LINK] Axe

[LINK]  Reeves

And this: [LINK] Gauger

Q: Who has reviewed these?

Ann: As you know, peer review is confidential and I do not know their names. They were qualified research scientists by no means all favorable to ID. More than that I cannot say. The process is rigorous. Many papers are turned down.

Q: From “BIO-Complexity, Purpose and Scope”:

Purpose: BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life. Because questions having to do with the role and origin of information in living systems are at the heart of the scientific controversy over ID, these topics — viewed from all angles and perspectives — are central to the journal’s scope.

To achieve its aim, BIO-Complexity is founded on the principle of critical exchange that makes science work. Specifically, the journal enlists editors and reviewers with scientific expertise in relevant fields who hold a wide range of views on the merit of ID, but who agree on the importance of science for resolving controversies of this kind. Our editors use expert peer review, guided by their own judgement, to decide whether submitted work merits consideration and critique. BIO-Complexity aims not merely to publish work that meets this standard, but also to provide expert critical commentary on it.
Ann: We have reviewers on both sides of the question and invite anyone who is qualified to participate. As you can guess, the problem is that we are being stonewalled. We have applied to mainstream journals and they are returned without being considered.

Q: Ann Gauger, you just said you don’t know who reviews what.

Ann: I don’t. But if you’ve been through peer review yourself, you know that you can get a general feel for the attitude of the reviewer without knowing their name.

Q: “Reviewing” and publishing in a specially protected environment basically makes them whiff of cargo-cult science and deliberate attempts at deception. They won’t win any scientific case that way, just take in gullible lay people.

Ann: Let me respond to your accusation of cargo-cult science and deception. BIO-Complexity is not the first journal to be founded to advance a controversial case. From Wikipedia [regarding the journal Nature] — you can check their sources:

“…Nature was conceived, born, and raised to serve polemic purpose.”[12] Many of the early editions of Nature consisted of articles written by members of a group that called itself the X Club, a group of scientists known for having liberal, progressive, and somewhat controversial scientific beliefs relative to the time period.[12] Initiated by Thomas Henry Huxley, the group consisted of such important scientists as Joseph Dalton Hooker, Herbert Spencer, and John Tyndall, along with another five scientists and mathematicians; these scientists were all avid supporters of Darwin’s theory of evolution as common descent, a theory which, during the latter-half of the 19th century, received a great deal of criticism among more conservative groups of scientists.[14] Perhaps it was in part its scientific liberality that made Nature a longer-lasting success than its predecessors. John Maddox, editor of Nature from 1966 to 1973 as well as from 1980 to 1995, suggested at a celebratory dinner for the journal’s centennial edition that perhaps it was the journalistic qualities of Nature that drew readers in; “journalism” Maddox states, “is a way of creating a sense of community among people who would otherwise be isolated from each other. This is what Lockyer’s journal did from the start.”[15] In addition, Maddox mentions that the financial backing of the journal in its first years by the Macmillan family also allowed the journal to flourish and develop more freely than scientific journals before it.[15].”
So spare me your sneers.

Q: Ann Gauger, I expect their eventual success rested on the veracity of their science.

Ann: And so we will let time tell.

Q: Not to mention their intellectual integrity and honesty.

Ann: No — read the history of the X Club. And I thought our conversation was honest and above ad hominems.

Q: Questioning honesty is not ad-hominem. It relates directly to the trustworthiness of what they are saying. Criticising an organisation or an individual for being naughty in a way that is unrelated to what they are arguing — that would be ad-hom.

Ann: Ad hominem attacks can take the form of overtly attacking somebody, or more subtly casting doubt on their character or personal attributes as a way to discredit …

Q: Ann Gauger, as I said, the exception is when we question their honesty and integrity in making statements.

“X is a habitual liar, so you cannot trust what he says about anything.” This is not ad-hom.

“X is smelly, so you cannot trust what he says about anything.” This is ad-hom.

Ann: Casting doubt on the integrity of an individual does not address the argument, it dismisses it, just as you dismiss our papers because of where they were published. Why not read them and judge them on their own merits?

And why not take my arguments as truthful, not deceptive, based on the evidence, not any prejudgment or label?

How are we to get an adequate hearing in the face of such prejudice?

Q: Ann Gauger, your history is against you. Starting with the Wedge document. My “prejudice” is based on years of investigating the claims of creationist/ID enthusiasts, and by learning about their underhanded tactics for infiltrating academe. You have brought all this upon yourselves.

Ann: Well, apparently, you know something about our history that I don’t. Infiltrating academe? What does that mean?

Ann: It took me a while to find this, but your accusation of infiltration reminded me of a quote from a book I had read:

[T]he process of conversion involved much hard lobbying by Huxley, Hooker and other naturalists who jumped to the defense of the theory. Huxley’s real triumph was in gradually extending the influence of those who shared his aversion to the design argument within the community of professional scientists. This influence was at last beginning to expand, and Huxley networked endlessly to ensure that people sympathetic to his position got the jobs that were opening up in the universities and elsewhere. It became unfashionable for a scientist to make open appeals to the supernatural, even if he (and they were still almost all men) believed in a Creator.

(Peter J. Bowler, Monkey Trials and Gorilla Sermons: Evolution and Christianity from Darwin to Intelligent Design (Cambridge, Massachusetts: Harvard University Press, 2007), pp. 38-39)
Q: Ann Gauger, do you have any evidence that Huxley was underhanded? Dishonest?

Ann: There’s more to the quote that I don’t have available to me now. Do you have such evidence?

Q: Nope.

Ann: And with regard to ID?

Q: I’ve already mentioned the Wedge document. It starts there.

[What’s the so-called “Wedge document” he keeps mentioning? See here . –Editor]

Ann: One more piece, this time about Darwin[LINK]:

Darwin’s picture of himself, and our dominant picture of him, as a pure scientist, slow at writing, poor at arguing, concerned only with the truth or with the judgment of a small group of experts and indifferent to public opinion, is a picture taken in the earlier part of his career and is irreconcilable with his motives and actions in the years of public controversy. Darwin’s self-image ignores his extensive efforts to proselytize, to simplify the bases for believing in evolution, and to broaden his base of support. Darwin’s failure to integrate his rhetorical action with his self-understanding as a scientist has powerfully reinforced a positivist interpretation of his achievement as merely the inevitable consequence of a superior account.

Finally the study has implications for our understanding of the ethics of scientific rhetoric. Given that science and civilization exist in an interdependent relationship, how far is it legitimate for science to mask its opposition to dominant cultural values? To what extent does the ethic of science demand truthfulness, when the price of truth may be a temporary, or perhaps even sustained, reaction against a particular scientific theory? In his use of Gray’s essays, does Darwin’s encouragement of the public to draw a theological conclusion beneficial to his persuasive aim, but counter to his personal convictions, make him cynical or dishonest? Or should we see him as acting to create a cultural environment beneficial to science and perhaps in time conducive to a more enlightened understanding of religion? It seems that however we interpret Dar win’s rhetorical strategies and tactics, we are left with the discomfiting realization that Darwin the historical truth bearer was not always Darwin the historical truth teller. The ethical obligation peculiar to rhetoric is to give truth effective advocacy.
Ann: The people I work with are men of integrity and honesty. I am not aware of any deception or misrepresentation on their part.

You may disagree with their motives or conclusions. But then as should be clear above, Huxley and Darwin were fighting their own cultural battle, and not always openly, with some deception involved. There is the story of how Darwin managed to get his theory admitted before the Royal Society at the same time as Wallace by lobbying with friends and Lyell. Your indignation over the Wedge document, which I have not read by the way, is mainly cultural, I suspect, and not because anyone was proposing underhanded science….

Ann: Gotta go. It’s been fun.

Fear dumb people not smart machines?

Bill Dembski on the AI Boogeyman, and the Real AI Danger
Evolution News | @DiscoveryCSC

On a new episode of ID the Future, Andrew McDiarmid reads an excerpt from a speech prepared by philosopher, mathematician, and trailblazing design theorist William Dembski for the launch of the 

Walter Bradley Center for Natural and Artificial Intelligence.

Download the podcast or listen to it here.

Dr. Dembski asks whether we need to worry about an AI takeover. He says no, there’s no evidence that artificial intelligence (AI) could reach that level, or achieve consciousness, while on the other hand there is mounting evidence from both philosophy and the field of artificial intelligence technology that it cannot and will not.

“The real worry,” Dembski says, “isn’t that we’ll raise machines to our level, but that we’ll lower humanity to the level of machines.”

Big tobacco:A prelude to big marijuana?

Philip Morris v. Uruguay: Will investor-State arbitration send restrictions on tobacco marketing up in smoke?

MATTHEW C. PORTERFIELD & CHRISTOPHER R. BYRNES – July 12, 2011

For nearly two decades, the tobacco industry has used international investment rules to challenge governmentrestrictions on cigarette marketing.  In 1994, R.J. Reynolds Tobacco Company threatened to bring a claim under the North American Free Trade Agreement’s (NAFTA) investment chapter as part of its successful lobbying campaign against Canada’s proposed “plain packaging” legislation, which would have required that all cigarettes be sold in standardized packaging without logos or trademarks. More recently, Philip Morris has brought an investor-state claim challenging Uruguay’s restrictions on cigarette packaging, and formally threatened the government of Australia with an arbitration claim in response to its packaging rules.[i]

Philip Morris’s challenge to Uruguay’s tobacco regulations raises a number of fascinating (although not entirely new) issues concerning international investment law, including the scope of fair and equitable treatment, the use of most favored nation (MFN) provisions to invoke more lenient procedural standards, and the availability of injunctive relief in investment arbitration. The legal basis of Philip Morris’s notice of claim against Australia has not yet been publicly disclosed, but the case promises to be closely watched in Australia and abroad.

Perhaps even more interesting, however, will be the response of governments to this use of investor-state arbitration in the politically sensitive context of tobacco regulation.  Philip Morris has lobbied the United States Trade Representative (USTR) to include strong investment protections for tobacco trademarks in the proposed Trans-Pacific Partnership Agreement (TPPA).  Australia, in turn, has announced that it will oppose the inclusion of investor-state arbitration in its future free trade agreements, including the TPPA, due in part to the threat of challenges to its proposed plain packaging rules.  The reaction to Australia’s stance by the United States government, which is legally prohibited from promoting tobacco exports or seeking the removal of non-discriminatory tobacco regulations, will merit particular attention.

Threat of investment arbitration used against Canada’s plain packaging proposal 

Canadian parliamentarians first seriously considered plain packing as a regulatory option in early 1994.  The tobacco industry had just won a lengthy campaign to roll back high tobacco taxes, and Parliament sought to offset the health effects of lower taxes by implementing plain packaging regulations.[ii]

Given the widespread concern for tobacco’s negative health effects, the tobacco industry was wary of debating plain packaging as a health issue.  The industry saw trade and investment rules, especially those included in the recently enacted NAFTA, as an effective way to frame plain packaging as a legal issue divorced from health concerns.[iii]  Relying on NAFTA’s investment chapter, R.J. Reynolds Tobacco Company sent a memorandum to the House of Commons Standing Committee on Health arguing that plain packaging would constitute an illegal expropriation of a legally protected trademark, requiring Canada to pay hundreds of millions of dollars in compensation.[iv]

The mere threat of investment arbitration had a powerful impact on Parliament’s deliberations on plain packaging.  Although it was the Canadian Supreme Court’s invalidation of Canada’s Tobacco Products Control Act in 1995 that ultimately put the plain packaging debate to rest, the NAFTA threat is widely believed to have deterred the government from taking legislative action on plain packaging prior to the Court’s ruling.[v]  

Philip Morris v. Uruguay 

On 19 February 2010, Philip Morris filed a request for arbitration against Uruguay with the International Centre for Settlement of Investment Disputes (ICSID).  Philip Morris alleges that recent tobacco regulations enacted by Uruguay violate several provisions of the Switzerland-Uruguay bilateral investment treaty (BIT).[vi]   Specifically, Philip Morris is challenging three provisions of Uruguay’s tobacco regulations: (1) a “single presentation” requirement that prohibits marketing more than one tobacco product under each brand,[vii] (2) a requirement that tobacco packages include “pictograms” with graphic images of the health consequences of smoking (such as cancerous lungs),[viii] and (3) a mandate that health warnings cover 80% of the front and back of cigarette packages.[ix]

All three measures, Philip Morris argues, violate Article 3(1) of the BIT, which prohibits subjecting investments to “unreasonable” measures, because they are overbroad and bear no rational relationship to their purported public health objectives.[x]  Philip Morris further alleges that the single presentation requirement constitutes an expropriation of Philip Morris’s trademarks by prohibiting their use on multiple brands.[xi]

The scope of fair and equitable treatment

Philip Morris’s most interesting claims implicate one of the more persistent areas of debate in international investment law:  the scope of the rights provided under the “fair and equitable treatment” provisions of investment treaties.  The most restrictive interpretation of this language (and the position that the United States has taken since 2002) is that it merely reflects the customary international law standard of protection that is already guaranteed to foreign investors under the right to the “minimum standard of treatment” under international law.

Philip Morris, however, asserts some of the more expansive interpretations of fair and equitable treatment, including a right to a “stable and predictable regulatory framework.”  This right, Philip Morris argues, was violated by Uruguay’s single presentation and pictogram requirements, which frustrated its “legitimate expectations” concerning its investment in Uruguay.[xii]  Philip Morris also argues that Uruguay has denied it fair and equitable treatment by violating the World Trade Organization’s Agreement on Trade Related Aspects of Intellectual Property Rights (TRIPS), implicitly adopting the controversial position that fair and equitable treatment includes rights under treaties in addition to customary international law.[xiii]

Philip Morris’s request for arbitration also raises interesting procedural questions concerning the use of MFN clauses to avoid procedural obligations and the availability of injunctive relief in investment arbitration.

Injunctive relief as a remedy in investor-state arbitration

In addition to monetary damages, Philip Morris is requesting that the tribunal order Uruguay to suspend the application of the challenged regulations.[xiv]   Investor-state tribunals typically provide relief in the form of monetary damages; there has been relatively little discussion of the availability of injunctive relief.  At least one prominent commentator, however, has concluded that “the [ICSID] Convention’s drafting history indicates that an ICSID tribunal has the power not only to award monetary damages, but also to order a party to perform a specific act or to desist from a particular course of action.”[xv]

Using MFN provisions to bypass procedural requirements

Prior to bringing an investor-state claim, Article 10 of the Switzerland-Uruguay BIT requires an investor to attempt to negotiate a resolution of a dispute with the host country for at least six months, and then to attempt to litigate the dispute through the domestic courts of the host state for at least eighteen months.  Philip Morris argues, however, that it need not comply with either requirement because the BIT contains an MFN provision that entitles it to the standard of treatment that Uruguay provides to investors from other countries under BITs that permit investors to proceed directly to arbitration.

A similar strategy was used in the well-known Maffezini v. Spain arbitration to bypass a provision in the Argentina-Spain BIT that requires an investor to pursue available domestic remedies for at least eighteen months before bringing an arbitration claim.[xvi]  Other tribunals have rejected attempts to use MFN clauses in investment treaties to gain access to more favorable dispute settlement provisions in other agreements.[xvii]

Tobacco regulations and the Trans-Pacific Partnership Agreement

The potential use of investment arbitration to challenge tobacco regulations has also become a source of controversy in the negotiations on the TPPA, a free trade agreement being negotiated by Australia, Brunei, Chile, Malaysia, New Zealand, Peru, Singapore, the United States and Vietnam.   Philip Morris has moved aggressively to use the TPPA negotiations to limit restrictions on tobacco marketing.   In comments submitted to USTR, Philip Morris argued that Australia’s plain packaging regulations would be “tantamount to expropriation” of its intellectual property rights, and complained of the broad authority delegated to Singapore’s Minister of Health to restrict tobacco marketing.[xviii]  In order to address these “excessive legislative proposals,” Philip Morris urged USTR to pursue both strong protections for intellectual property and inclusion of the investor-state dispute settlement mechanism in the TPPA.

More recently, Philip Morris served the government of Australia with a notice of claim, setting in motion a three-month period of negotiation before arbitration proceedings can be commenced. Philip Morris is relying on the Australia-Hong Kong BIT, as its Australian operations are owned by the Hong Kong-based Philip Morris Asia Limited. Announcing the notice of claim on 27 June 2011, a spokesperson for the company said “damages may amount to billions of dollars”.

Australia renounces investor-state arbitration and greater rights for foreign investors

Even before its notice of claim was sent in June, Philip Morris’s aggressive use of investment law to challenge tobacco regulations may have backfired.   In April, Australia’s government announced that it would no longer support the inclusion of investor-state arbitration in its free trade agreements, explicitly linking its new position to the attempts to “limit [Australia’s] capacity to put health warnings or plain packaging requirements on tobacco products . . .”[xix]

Significantly, Australia also indicated that it would support equal treatment for foreign and domestic investors, but would oppose provisions in future agreements that would provide foreign investors with greater rights.  This stance echoes the Calvo Doctrine that many Latin American governments once espoused, as well as the United States Congress’s mandate that U.S. investment agreements should not provide foreign investors with greater substantive rights than those enjoyed by domestic investors.[xx]

Australia’s initiative on plain packaging is consistent with its status as a Party to the World Health Organization Framework Convention on Tobacco Control (FCTC), the world’s first global public health treaty.  Article 11 of the FCTC requires all signatories to enact strong packaging and labeling regulations, consistent with those enacted in Uruguay and proposed in Australia.[xxi]  Another prospective member of the TPPA and signatory to the FCTC, New Zealand, has indicated that it may also impose plain packaging regulations on tobacco products,[xxii] further heightening tension over the issue in the TPPA negotiations.

Conflict between investment rules and U.S. law supporting tobacco regulations?

 The controversy over plain packaging regulations and investor-state arbitration puts the United States in an awkward position in the TPPA negotiations.   Since 1997, an amendment to the annual appropriations bill sponsored by Congressman Lloyd Doggett has prohibited USTR from using government funds—

to promote the sale or export of tobacco or tobacco products, or to seek the reduction or removal by any foreign country of restrictions on the marketing of tobacco or tobacco products, except for restrictions which are not applied equally to all tobacco or tobacco products of the same type.[xxiii]

Executive Order 13193, signed by President Clinton in 2001, similarly prohibits U.S. agencies from promoting the sale or export of tobacco or seeking to reduce or remove foreign governments’ advertising restrictions on tobacco products.[xxiv]

Arguably, USTR routinely violates these restrictions by negotiating provisions in U.S. trade agreements that potentially restrict the ability of governments to regulate the marketing of tobacco products.  U.S. FTAs typically include many of the same provisions that Philip Morris is currently invoking in its arbitration against Uruguay, including protection for intellectual property rights, investor-state dispute settlement, a prohibition on uncompensated expropriation, and a guarantee of “fair and equitable treatment.”  Nevertheless,   in light of the significant media coverage that Australia’s stance on plain packaging and investor-state arbitration has received, it appears likely that USTR’s compliance with the Doggett Amendment and Executive Order 13193 in the TPPA negotiations will attract substantial scrutiny.

Conclusion

The tobacco industry’s aggressive use of investment rules could prove to be an effective strategy for opposing restrictions on tobacco marketing.  Yet given the widespread support for tobacco regulations, it seems just as plausible that this strategy could result in a backlash against investor-state arbitration.   Accordingly, the growing tension between tobacco regulations and investor-state arbitration should be a subject of interest not only for tobacco companies and public health advocates, but also for anyone interested in the future of investor-state arbitration.

Authors

Matthew C. Porterfield is a Senior Fellow and Adjunct Professor at the Georgetown University Law Center’s Harrison Institute for Public Law.  Christopher R. Byrnes is a J.D. candidate, 2012, at Georgetown University.

How the consensus' gatekeepers got egg on their face.

James Tour on OOL science's circus.

On Origin of Life, Synthetic Chemist James Tour Delivers Chastisement to Jeremy England
David Klinghoffer | @d_klinghoffer  

As a postscript to Brian Miller’s  reply to MIT physicist Jeremy England, see this from the famed synthetic organic chemist James Tour, writing for the online journal Inference. In“An Open Letter to My Colleagues,” Tour sets out this way:

Life should not exist. This much we know from chemistry. In contrast to the ubiquity of life on earth, the lifelessness of other planets makes far better chemical sense. Synthetic chemists know what it takes to build just one molecular compound. The compound must be designed, the stereochemistry controlled. Yield optimization, purification, and characterization are needed. An elaborate supply is required to control synthesis from start to finish. None of this is easy. Few researchers from other disciplines understand how molecules are synthesized.

His colleagues are fooling themselves if they imagine otherwise. He gets around to England, not naming him except in a footnote, at the end:

If one understands the second law of thermodynamics, according to some physicists,15 “You [can] start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.”16

The quote, remarkably, is from Jeremy England in an interview with Natalie Wolchover for Quanta. Tour also cites England’s article “Statistical Physics of Self-Replication,” in the Journal of Chemical Physics, and one of the most absurdly titled God-bashing articles we’ve come across, “God is on the Ropes: The Brilliant New Science That Has Creationists and the Christian Right Terrified,” by Paul Rosenberg writing for Salon. Rosenberg quotes England from the same Quanta article, “[U]nder certain conditions, matter inexorably acquires the key physical attribute associated with life.” Oh, really, does it?

Tour goes on, referring to the notion that random atoms will become a plant if given plenty of light and plenty of time:

The interactions of light with small molecules is well understood. The experiment has been performed. The outcome is known. Regardless of the wavelength of the light, no plant ever forms.

We synthetic chemists should state the obvious. The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense.

Beyond our planet, all the others that have been probed are lifeless, a result in accord with our chemical expectations. The laws of physics and chemistry’s Periodic Table are universal, suggesting that life based upon amino acids, nucleotides, saccharides and lipids is an anomaly. Life should not exist anywhere in our universe. Life should not even exist on the surface of the earth.17

It’s somehow more satisfying that England isn’t identified in the body of the article, but only in a footnote. That is a memorable instance of a senior scientist quietly taking a junior colleague out behind the woodshed. For more on the general subject, see Tour’s slashing 2016 lecture,  “The Origin of Life: An Inside Story.”

Darwinism's quest for a free lunch hits yet another dead end?

Conservation of Information and Coevolution: New BIO-Complexity Article by Ewert and Marks
Brian Miller  

In a  previous article I described Winston Ewert, Robert Marks, and William Dembski’s book Introduction to Evolutionary Informatics which identifies the limitations of evolutionary algorithms to find solutions for complex problems. The book demonstrates that this class of programs is only capable of achieving non-trivial results unless information about desired outcomes is programmed into them. For instance, a program designed to find the best strategy for playing checkers must have detailed information about the game programmed into its search method. It could not develop a strategy to play chess without altering the underlying algorithm to include new chess-related information.

This constraint is a direct result of No Free Lunch (NFL) theorems and the related law of  Conservation of Information. Attempts have been make to overcome this challenge by appealing to what are termed coevolutionary searches. However, as Ewert and Marks demonstrate in a new article for the journal BIO-Complexity, these algorithms do not escape the NFL barrier, so they are no more efficient on average than random searches.

Evolutionary algorithms typically follow a standard set of steps. They generate trial solutions to a problem, and then assign each trial some “fitness” value. These values are then used to determine how the next iteration of trials is generated for testing. The process continues until a target is found.

Ewert and Marks use the illustration of generating recipes for making pancakes. In this example, a trial recipe represents a list of the specific amounts of each ingredient and details of the cooking, such as burner setting and times. The assigned value corresponds to the prepared pancake’s taste, and it determines how new recipes are generated. The process continues until a pancake is created that meets some taste standard. The set of values associated with all possible trials is described as a fitness landscape, and the search algorithm must navigate its terrain looking for targets. For standard algorithms, all information needed to assign a fitness value is known. In contrast, for coevolutionary algorithms information is not fully known, so incomplete or “subjacent” information must often be used. That’s because the fitness landscape continuously changes due to the presence of other organisms or other contingent factors.

This difference can be illustrated in terms of an examples from biological evolution. A standard evolutionary algorithm would correspond to an organism having a specific “fitness” which remains fairly constant in most situations. For instance, that of a desert plant might relate to such innate abilities as conserving water and processing sunlight. A computer program could model the plant’s fitness using related variables, such as the plant’s mass and the amount of chlorophyll produced in its leaves. These variables would fully determine the assigned fitness value. In contrast, a coevolutonary process would correspond to the fitness changing over time due to such factors as interactions with other species and details of the physical environment. For instance, chemicals in the skin could provide greater or lesser protection from different predators, and the shape of the plant could prove more or less helpful in different settings.

To model this increased complexity, the algorithms generate a query matrix where a row is assigned to each candidate solution, and each column corresponds to a different factor affecting fitness such as interactions with a particular species. Many cells in this matrix are often not known, whether due to computational or other practical limitations, so various methods are employed to assign each trial solution (row) an aggregate value based on the limited knowledge. The algorithm then proceeds as with traditional models. Many have claimed that coevolutionary programs can find solutions to a wide variety of problems more quickly on average than random searches, thus overcoming the restrictions of the NFL theorems. In other words, they eliminate the need for programmers to provide problem-specific “active information” to guide searches.

To test this claim, Ewert and Marks measured the performance of various coevolutionary algorithms for a variety of problems. They found that they could at best match the performance of traditional “full-search” methods, and they typically performed worse. Their article also describes how claims to the contrary were based on research that focused on solving very simple problems or that designed experiments in such a way as to provide hidden information to assist in finding targets. Therefore, coevolutionary processes cannot overcome NFL limitations, as they also require problem-specific information to perform properly.

These results have direct implications for Darwinian evolution. Biologists often claim that coevolutionary interactions between different species or species and the environment can alter the underlying fitness landscape in such a way as to drive evolutionary changes. A classic example is the proposed coevolution of bees and flowering plants. Many plants need insects as carriers for their pollen. As a result, the presence of insects places selective pressure on the plants to produce smells, colors, and nectar to attract them. In turn, the presence of the plants places selective pressures on the insects to move toward the plants’ signals to obtain the food supply. In addition, insects are selected for thicker hairs on their legs to capture more pollen. They can then fertilize more plants resulting in a greater food supply. Such scenarios may sound plausible, but they only result in trivial adjustments to preexisting structures.

In contrast, complex innovations, such as new body plans, radical innovations which, in turn, require large amounts of new information.The environment is often claimed to provide this new information, which is believed to be hidden in the fitness landscapes coupled to coevolutionary interactions. However, this research by Ewert and Marks directly challenges the claim. The search space corresponding to biological forms is vastly greater than what could be searched through random mutations in the offspring of any species. And natural selection cannot help without being provided large amounts of information on where new forms reside. For coevolutionary processes are no more efficient at solving problems than traditional evolutionary algorithms, and the latter are no more efficient on average than random searches.