Testing fundamental evolutionary hypotheses


Testing fundamental evolutionary hypotheses by David Penny, Michael Hendy and Anthony Pool was published in Journal of Theoretical Biology volume 223, pages 377-385 in 2003. Penny et al show that ‘Intelligent Design’ can be formulated as a testable hypothesis but this requires us to formulate motivation(s), means and/or opportunity to restrain the explanatory power of an ‘intelligent designer’. Additionally, they show why various potential ID hypotheses can be rejected based on the experimental evidence. Until ID proposes other hypotheses, common descent seems to remain the best hypothesis available. Since the Geoscience Research Institute (GRISDA) proposes an alternative theory of ID (multiple independent origins) I will explore this hypothesis and show that again the data do not bode well for ID.

Sober and Steel (J. Theor. Biol. 218, 395-408) give important limits on the use of current models with sequence data for studying ancient aspects of evolution; but they go too far in suggesting that several fundamental aspects of evolutionary theory cannot be tested in a normal scientific manner. To the contrary, we show examples of how some alternatives to the theory of descent can be formulated in such a way that they lead to predictions that can be evaluated (and rejected). The critical factor is a logical formulation of the alternatives, even though not all possible alternatives can be tested simultaneously. Similarly, some of the limits using DNA sequence data can be overcome by other types of sequence derived characters. The uniqueness (or not) of the origin of life, though still difficult, is similarly amenable to the testing of alternative hypotheses. Testing fundamental evolutionary hypotheses by David Penny, Michael Hendy and Anthony Pool

Penny et al discusses various hypotheses

1. Viruses from space

This is a test of Hoyle and Wickramasinghe’s claim that influenza viruses arrive via comets. Penny et al show that this claim has to be rejected.

2. Intelligent design

We can test the theory of descent versus a theory of individual creation of species–with each species being intelligently designed for its environment. Consider photosynthetic enzymes from plants living in a hot, dry desert (a cactus and a desert grass) with those from a moist-temperate grass. A wise creator might design similar photosynthetic enzymes for leaves functioning under hot dry conditions (the cactus and a desert grass). This version of intelligent design would predict the following rooted tree for these enzymes: ((cactus, desert grass), temperate grass)–see Fig. 3A. This brings together enzymes from similar physical environments; under stress from high temperatures and strong water deficits. In contrast, the theory of descent predicts that the grass enzymes would be more similar: (cactus, (desert grass, temperate grass))–see Fig. 3B. This unites sequences sharing a more recent common ancestor, irrespective of their current physical environment. In practice, common ancestry gives the correct prediction for photosynthetic enzymes. Many similar tests can be designed. The logic is identical for comparing protein sequences in the hairs of polar bears and snow rabbits with, say, those of a rabbit in a warm environment. Under intelligent design, the proteins in the two species living under Arctic conditions could be created to give maximum insulation under freezing conditions. Thus, hair proteins from species living in the Arctic would be similar for functional reasons. This test may not have been done, but the point is that the theory of descent leads to testable predictions. It is possible for Intelligent Design to fudge predictions to make them identical to the theory of descent, but this is unsatisfactory. It provides no mechanism that leads to the observed data, and it leads to a creator appearing to be the ‘‘Great Deceiver” who deliberately misleads rational humans. Testing fundamental evolutionary hypotheses by David Penny, Michael Hendy and Anthony Pool

On GRISDA we find the following comments on this paper:

Comment. This paper illustrates the difficulty all of us have in responding to criticisms made by persons with presuppositions that clash with our own. I will discuss three problems with the arguments presented. First, Penny et al. argue that the best method for tree construction is the method that gives the most congruent results from different data sets. However, this is true only if the species actually do share a common ancestor. If they have separate origins, the best method might be the one that shows the greatest conflict in the different trees. Conflict among evolutionary trees based on different data sets is so widespread and common that one may prefer the conclusion that common ancestry has been falsified. GRISDA comments

That conflicts between different datasets are so widespread and common is a common fallacy, lacking as usual in any meaningful substance.

Theobald shows that

In real-life phylogenetic analyses, shared derived characters may be in conflict with other derived characters. Thus, objective methods are required for resolving this character conflict (Kitching et al. 1998, Ch. 1; Maddison and Maddison 1992, p. 49).

In the past 40 years, several algorithmic methods have been devised to resolve such instances of character conflict and to infer correct phylogenetic trees (Felsenstein 2004, Ch. 10). The following sections outline some of the most successful of these methods. Each method attempts to infer a phylogeny from existing data, and each has its respective strengths and weaknesses. Years of empirical testing and simulation have shown that, in general, these different algorithms, each with very different underlying assumptions, converge on trees that are highly similar when judged statistically (Li 1997, Chs 5 and 6; Nei and Kumar 2000, Chs 6, 7, and 8). 29+ Evidences for Macroevolution by Douglas Theobald on Talkorigins

Second, there is an inconsistency in one of their arguments. In discussing how to test for common ancestry, Penny et al. make the statement that “a minimal-length Steiner tree can be calculated for any data…”. This statement is followed later in the same paragraph by a defense of their ability to test the theory of descent for mammals because it “allows a comparison against a null alternative (that there was no treelike information in the data).” A null hypothesis (there is no treelike information in the data) that must be rejected in every case (because a tree can be constructed for every data set) can hardly serve as a test of a hypothesis. GRISDA comments

This assertion about Steiner trees misses the point that Penny et al are making totally. What Penny et al argue is that the hypothesis of a rooted Steiner tree can be compared with a hypothesis of no rooted tree to see which one gives the best match. Just like a correlation coefficient can be calculated for any dataset larger than one sample point, this does not mean that correlation coefficients cannot serve to determine the best match given a particular hypothesis. Darwin’s theory provides for a theoretical foundation why one would expect a rooted Steiner tree, making the observation that a rooted Steiner tree is a better hypothesis than no tree, one in support of Darwinian theory. If ID proposes an alternative structure then let them present the hypotheses and analysis to support their claims.

Penny et al explain this in their paper

Our prediction from the theory of descent was that orthologous genes in mammals should lead to similar trees–they are expected to share the same evolutionary history. We found minimal-length trees from five protein datasets, and showed that the trees were much more similar than expected by chance. Testing fundamental evolutionary hypotheses by David Penny, Michael Hendy and Anthony Pool

Nothing contradictory. If there were no rooted tree structure one would expect the rooted Steiner trees from various genes to be no more similar than expected from chance.

Third, the alternative hypotheses for which tests are proposed seem more like straw men than real competing hypotheses. One alternative hypothesis is that influenza viruses have repeatedly come from outer space, rather than descending from a common ancestor. The other alternative hypothesis was that every species was created individually, optimally designed for its present environment. Neither of these hypotheses is taken seriously by those who are skeptical of common ancestry. GRISDA comments

The first hypothesis addresses claims of panspermia by Hoyle and Wickramasinghe, the second hypothesis shows how we need to define means. motives, opportunities to actually constrain ID. Until ID proposes testable hypotheses, one cannot blame scientists to formulate plausible hypotheses of ID. The hypothesis that species were designed optimally for its present environment seems hardly that illogical.

What would be more interesting would be a test of a hypothesis that there exist multiple independent lineages, each of which has diversified into numerous species. A hypothesis of this type seems to fit the data better than any competitor, notably including the hypothesis of a single common ancestor. GRISDA comments

As is often typical with ID ‘hypotheses’ it fails to be supported by any scientific analysis beyond the claim ‘a hypothesis of this kind seems to fit the data better than any competitor’. Conveniently this ignores the plausibility of common descent from multiple ancestors, such as Woese proposes. Darwin already speculated about this possibility and thus parsimony would reject the requirement of ‘a designer’ to explain these data. While the ID strawman of the Cambrian Period may give one the impression that multiple independent lineages arose and diversified, the actual data do not really suggest support for this creationist strawman.

Ironically, Penny et al do address the hypothesis of multiple common ancestors in their paper.

Useful references


Paul Nelson on Ontogenetic depth thread at ISCID comments on the Penny paper

As Charlie D has pointed out, on this discussion board and elsewhere, the deeper assumption of evolutionary reasoning – that is, deeper than universal common descent itself – is naturalism.

Let me recommend a couple of recent (fascinating) papers on this topic:

Elliott Sober and Michael Steel, “Testing the hypothesis of common ancestry,” Journal of Theoretical Biology 218 (2002):395-408.

David Penny, Michael D. Hendy, and Anthony M. Poole, “Testing fundamental evolutionary hypotheses,” Journal of Theoretical Biology 223 (2003):377-385.

A common fallacy seems to be to confuse methodological naturalism with naturalism. If Paul Nelson can propose a better hypothesis then he is free to show how his hypothesis performs relative to for instance ‘common descent”.

So far ID has remained (mostly) silent on any positive hypothesis of design. Btw we are still waiting on Paul to present the details of his ontogenetic depth claims.

Under the heading “Intelligent Design” in the Pendy et al paper reads the following statement:

“We can test the theory of descent against a theory of individual creation of species–with each species being intelligentlty designed for its environment”

The heading should not be “Intelligent Design” here, for ID theory is not commited to and does not argue, require, expect, predict, or so on, that each species is individually designed to fit its environment. For instance, ID theorists agree that species diversification, such as that which has occured on the Galapagos islands, is the result of evolution and not seperate moments of intelligent design or anything like that.

ID theorists simply are not committed to the “individual creation” of a species “intelligently designed for its environment.” This is either an argument for the falsification of some different form of a creation hyptothesis or a straw-man of ID.

T. Russ identifies the real problem with ID namely that it is not commited to any prediction. ID so far is mostly an argument from ignorance and as Penny shows, unless it presents specifics, scientifically meaningless. Of course when it presents specifics such as GRISDA suggests, it seems to be falsified.

Either way, things do not look to good.

What needs to be shown to conclude that ID is not a viable hypothesis is show that intelligent causes were not necessary to create the things in question; large bio-macromolecules (containing genetic programms for the building of proteins etc), complex structures which appear to have no functional transitionary forms (IC), and so forth. To falsify ID, all you must do is show that the design found in the natural world really is only apparent and explainable by a natural process such as evolution. So, therefore the entire evolutionary hypothesis and scientific project is seeking a falsification of the argument for design. This was the way in which Darwin first cashed out his theory and the way modern evolutionists cash it out today. If evolutionary naturalism is true than ID is false.

Problem is, many, yes many, think that intelligent causation is a far more adequate explanation for life’s complexity than what they believe as a failed evolutionary program. (of course these people are dismissed in exactly the sort of way which Thomas Kuhn argued that they would)

T. Russ

Moving the goalposts T. Russ:

T.Russ Wrote:

What needs to be shown to conclude that ID is not a viable hypothesis is show that intelligent causes were not necessary to create the things in question;

No such effort is needed since ID does not present any viable hypothesis. Notice that evolutionary hypotheses do not rely on a negative, namely to show that intelligent causes were not necessary but present their own and can be tested as such. T.Russ shows what is wrong with ID in an exquisite manner.

Confused by the appeal to ignorance so typical to ID, T. Russ now seems to require that science accepts the same faulty methodology

To falsify ID, all you must do is show that the design found in the natural world really is only apparent and explainable by a natural process such as evolution.

Not at all. Since ID presents NO hypotheses, and science presents testable hypotheses which do not rely on our ignorance, the requirement that science should step down to the level of ID is somewhat ironic if not insulting.

Problem is, many, yes many, think that intelligent causation is a far more adequate explanation for life’s complexity than what they believe as a failed evolutionary program. (of course these people are dismissed in exactly the sort of way which Thomas Kuhn argued that they would)

The ignorance of these supposedly ‘many’ should not be a reason to take their position seriously. That people have been misled to believe that ID has showed something it cannot is something which will eventually backfire on ID just like YEC’s claims backfire on so many. If these people believe that intelligent causation is a far more adequate explanation let them present a testable hypothesis that shows this to be the case. ID for the last decade or more has failed to present any such hypothesis.

Combine this with the failed theoretical foundations, the failure to present positive hypotheses, the failure to present even the basic calculations needed for the design inference for non trivial cases shows that ID is just a meaningless concept. Although it may serve its purpose of giving the impression to some of its faithful that it has scientific relevance. Bruce Gordon warned against ID rushing ahead of itself, Wimsatt objected strongly to the claims in NFL and its advertising. High expectations were set, and I can understand that many ID proponents still believe that ID will live up to its claims and promises but the outlook is quite dim. Just look at how T.Russ responds here to see that ID has no clothes.

I thought T. Russ had resolved to stay away from Panda’s Thumb until he had read, and was ready to respond to, Wesley’s essays detailing the failure of Dembski’s efforts.

How’s that coming, T. Russ?

The ignorance of these supposedly ‘many’ should not be a reason to take their position seriously.

If the contents of high school curricula depended on the scientific approach, this would be true. But those curricula depend on the desires of the many. And they matter.

If these people believe that intelligent causation is a far more adequate explanation let them present a testable hypothesis that shows this to be the case.

They don’t need to. Magic explains anything. No reason to appeal to evidence; no hypotheses or testing required. The error here lies in equating “adequate” with “justifiable” rather than “preferred.” Any proposal in accord with existing beliefs is adequate, and more than adequate.

Granted it lacks scientific relevance. Now, we need to elect and appoint officials who consider this lack of relevance to be itself relevant. It’s these officials alone who prevent Judge Roy “my beliefs override the law” Moore from being elected Supreme Court Chief Justice in my state; otherwise he’d be elected by acclamation.

Update: Yesterday Judge Roy Moore’s appeal to the US Supreme Court was rejected without comment, exhausting his appeal process. Moore said the high court was composed of “liberal hypocrites” and carefully did not rule out the possibility of running for State Supreme Court Chief Justice again in 2006. In Alabama, judgeships are elected and not appointed positions. I wouldn’t bet against him.

I hope nobody has even the slightest doubt how Roy Moore would rule, if he were called upon to consider inserting religion into science classes. He wouldn’t even require the “plausible deniability” that ID isn’t religion.

Ok, first off, Russell:

I am still a student and only occasionally check out pandasthumb just to keep up with whats going on. Yes, I still need to finish up on Wesley’s work and engage that whole debate with him. But sorry for the occasional post, I will try not to engage in anymore discussions here until I’m ready to talk about those old issues.… well… try.


The hypothesis which ID theorists present is that intelligent agent causation is a necessary component in the production of X. To see whether IAC was in fact necessary, the theorist must take into account all that he or she knows concerning X, the explanatory power of IAC, the explanatory power of evolutionary naturalism (or any -IAC type mechanism) and by eliminative induction or an abductive inference, select the best explanation for X. ID relies on knowing and being able to test the explanatory power of IAC and -IAC mechanisms against one another. For instance, in S. Meyers (probably by now well known) argument, ID as an inference to the best explanation for DNA, he discusses what exactly needs to be explained when discussing the origin of DNA, and that is, the origin of the sequence specificity of nucleotide bases (which do not follow an ordered repeating pattern based upon natural bonding affinities etc). Meyer then considers the available explanations for DNA SS. He consider a host of possibilities, chance, necessity, chance and necessity combined, self-organization, pre-biotic NS, RNA world hypotheses, and so on (all explanations which are -IAC mechanisms.) He finds these to be wanting because they cannot explain SS. He then considers what we know about the causal power of intelligent agents. Intelligent agents can and do specify sequences(arrange letters to form sentences, create computer programs, etc.)He then argues that X demands a mechanism which can produce SS, and that IAC is the best current explanation for SS, and therefore the best explanation for X. The only way he can do this of course is to take into account the knowledge of what IAC and -IAC are capable of. Since his argument for ID here is an abductive inference it follows that his hypothesis is falsified if new knowlege of -IAC mechanisms is found which changes the current knowledge concerning whether it can specify sequences of genetic information. (create information)

You can read all this as an argument from ignorance, or as an argument from what we now currently know. (we know about DNA/SS, what IAC can do and what -IAC cannot do)I guess it all depends on which of the following options you chose to take. Do you base the acceptance of current hypotheses upon the knowledge that we currently have or on the future possibility that non-intelligent mechanisms will be found able to produce the hallmark signature of intelligent agents. It seems likely that the decision here (in this case of ID verses -ID) will most likely be mandated by your philosophical/religious disposition. For, if you already desire that anything at all consistent with GOD be out of the equation, you will always hold out for a future naturalistic explanation. Call it “naturalism of the gaps.” If you possess a different philosophical disposition, you might be open to the consideration of ID. Right now, I am siding with Meyer and the ID theorists. If Science changes and makes some new discoveries, I will have to follow them wherever they lead. If everytime somebody proposed an explanation based on current knowledge should we ignore them because of the possibility that they might not be right due to some unexpected future findings…nah, maybe we should ignore them because their argument seems repugnant to us…oh wait, good thing we are talking about science here.

Sorry for this quick and rushed answer (exam tomorrow, but I didn’t want to be ridiculed for not quickly responding :( )And sorry I will not be able to respond, as to the request that I honor my statements concerning reading up on Wesley which I made some months ago.

T. Russ

Off topic, but this discussion might amuse Pim.

You can read all this as an argument from ignorance, or as an argument from what we now currently know

That combined with an eliminative approach IS an argument form ignorance. Since the ID proponent fails to present a hypothesis of what an intelligent designer can and cannot do, it cannot even be an hypothesis. It all relies on the ability of the IDist to describe plausible natural pathways and its the ignorance, not the knowledge which leads the ID proponent to conclude design EVEN though in principle natural pathways may exist. So in other words, we do know that natural mechanisms can explain the observations in principle but we do not really present any hypotheses of ID to compare with other hypotheses. T Russ tries to call the scientific approach naturalism of the gaps but his argument is based on the flawed premise that science relies on naturalism rather than methodological naturalism, a common conflation by ID proponents. In other words, on the one hand ID proponents point to science appealing to Intelligent Design (archaeology, SETI, criminology, etc) and on the other hand they want to argue that science does not consider ID hypotheses. Present us the means, motives and opportunities of your best IDer and lets compare it with scientific hypotheses. ID so far, lacking fully in mechanisms, pathways etc relies on ignorance and is thus scientifically speaking irrelevant.

And nothing T Russ has argued changes this simple observation. We are not ignoring arguments, we are pointing out that ID presents none beyond the ususal ‘well, God (favorite IDer) could have done it’. But the issue is not that God could have done it, we all accept this. What the issue is such an explanation can be formulated in a scientifically meaningful manner. Without means, motives, opportunities or other ways to constrain the hypothesis we have to reject it as non scientific especially when compared to scientific hypotheses which seem to be far more plausible. The problem is that the IDer cannot and will not present a positive hypothesis exactly because it means that he has to constrain the designer involved. And unlike natural processes, there exist no such positive hypothesis for ID’s designer. Unlike ID, science however can and regularly does infer intelligent design in their search for life, archaeology and criminology. As Gary Hurd has shown archaeology, SETI, criminology however do not use the appeal to ignorance approach chosen by ID. That ID is meaningless scientifically is evidenced by its inability to present any positive hypothesis. In addition, their theoretical arguments are fundamentally flawed as many have shown by now.

Nothing much remains, I’d say other than faith (different philosophical disposition) …

Hi Tim, good to see you around. Yes, that is quite amusing.

RE: the T. Russ - PvM dialog:

Does this proposal hold water?

“All physical sciences, including biology, ultimately get down to the physical arrangement of matter, and matter-energy interactions.”

We humans, in order to effect our intelligent designs, require a large (but finite) number of moving parts with which to interact with matter and energy.

My question to IDers: how many moving parts does the Intelligent Designer have?

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