Intelligent Design

YouTube’s “C0nc0rdance” Reassures Us That The Evolution Of Chemotaxis Is Well In Hand

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I recently published an article on the marvelous design and engineering which undergirds the bacterial chemotaxis system. Since then, a notorious atheist who posts regular videos on YouTube under the alias “C0nc0rdance“, as well as “agentorange20” (under the latter, he identifies himself as Zachary Moore), has posted a rebuttal. This is a brief response to that rebuttal.

The extent to which two-component regulatory systems, or the chemotaxis system in particular, are irreducibly complex lay beyond the remit of my previous article, the purpose of which was to highlight the clear engineering analogues. With many of these signalling systems, there is an element of redundancy, with feedback and overlapping systems so as to make things stable and robust to error. As a result, there are often multiple versions that can still get the job done. Such systems are well designed — and detectably so — but there is no requisite for them to be irreducibly complex. However, it is my opinion that some subcomponents of the chemotaxis system may possibly be legitimately described as irreducibly complex (more on this to follow).

Such associated design and engineering principles associated with this system are obvious to those who are not pushing a materialist agenda. For example, one paper published in May of this year stated that,

Describing this pathway mathematically as a dynamical system can be facilitated by using tools from control theory. For example, it has been shown that the adaptation mechanism in the E. coli model is a particular example of integral control, a feedback system design principle used in control engineering to ensure the elimination of offset errors between a system’s desired and actual signals, irrespective of the levels of other signals.

One can discuss the clear design hallmarks pertinent to the system without even talking about the problems with the evolutionary account. The paper continues,

One of the different pathway configurations that is possible in this system has similarities to a feedback architecture commonly found in engineering control systems termed cascade control, which is usually employed when the process to be controlled can be split into a slow ‘primary’ sub-process ( in Figure 1) and a faster, secondary sub-process ( in Figure 1). […] In fact, cascade control is employed as a design principle in several engineering systems such as aircraft pitch control and industrial heat exchangers.

Moore raises four complaints with regards this system and irreducible complexity. Two of those complaints are relevant only to common descent (and not the grander thesis of neo-Darwinism that unguided mutation/selection are adequate to account for the system). Since ID is consistent with both common and uncommon descent, I will address the two points which are relevant to the adequacy of respective explanations.

Moore’s first complaint is that not all bacteria have the full pathway which I described. Before getting into the specifics, it is worth noting that irreducible complexity, as defined by Michael Behe in Darwin’s Black Box, does not entail that no simpler systems which perform the same job exist. In fact, Behe made this quite explicit. On page 43, Behe wrote,

To feel the full force of the conclusion that a system is irreducible complex and therefore has no functional precursors, we need to distinguish between a physical precursor and a conceptual precursor. The trap described above is not the only system that can immobilize a mouse. On other occasions my family has used a glue trap. In theory, at least, one can use a box propped open with a stick that could be tripped. Or one can simply shoot the mouse with a BB gun. These are not physical precursors to the standard mousetrap, however, since they cannot be transformed, step by Darwinian step, into a trap with a base, hammer, spring, catch and holding bar.

Similarly, it makes no sense to say that an automobile does not require an engine because one can use a bicycle! In like-manner, there are simpler ways to construct a flagellum. But that does not entail that a given flagellar system is not irreducibly complex. In the specific case which concerns us here, there may be alternative chemotaxis systems — but that does not nullify the irreducible complexity for the specific example that I described.

Another misconception which warrants clarification is the view that, for a system to be irreducibly complex, all of its subcomponents must be indispensable for the system’s overall functioning. But this is not the case. Contrary to this common misconception, irreducible complexity only requires that a subset of a given system’s components be indispensible.

Now, as Moore correctly notes, there is a significant amount of variation on chemotaxis systems. The pathway is best understood in the Gammaproteobacteria: a class of bacteria which includes E. Coli (the most extensively studied example) and Salmonella enterica. It is this class to which my previous discussion of the chemotaxis system pertained. A substantially less amount of data is available for other species of bacteria. Although individual genes bear homology to their Gammaproteobacteria counterparts, the pathways are somewhat mechanistically different. Furthermore, while general features of excitation remain conserved among bacteria and archaea, many of the more specific features are fairly diverse. One considerably more complex system than that of E. Coli is that of Bacillus subtilis (which you can read about here or here).

In E. coli, as discussed previously, chemoeffectors bind to the receptors and cause a conformational change in the methyl accepting chemotaxis proteins (MCPs). This conformational change is detected by CheA and CheW. This subsequently causes a change in the rate of autophosphorylation of CheA. CheA-P transfers phosphate groups to CheB and CheY. When CheY-P interacts with the switch, tumbling is induced. CheB-P acts as a methylesterase to remove methyl groups from the MCPs genearating methanol. CheR acts as a methyltransferase and methylates the MCPs. CheB thus brings about adaptation to the simuli by modifying the degree of methylation of the MCPs such that the rate of CheA autophosphorylation returns to the level it was at prior to the stimulus. CheZ acts to destroy the chemotactic signal by dephosphorylating CheY. In B. subtilis, the core control strategy for signal processing is very similar. However, B. subtilis possesses two additional feedback loops which provide an added layer of regulation. Moreover, although the proteins involved in both organisms are the same, the network structures are somewhat different.

So, in what ways are the pathways different between E. coli and B. subtilis? Rao et al. (2004) illustrate this with the aid of the following diagram:

chemotaxis e coli vs b subtilis.png

The figure legend reports,

(A) E. coli. (B) B. subtilis. Both organisms respond to extracellular signals by regulating the activity of the CheA histidine kinase. CheA is coupled to transmembrane receptors (MCP) by an adaptor protein CheW. Chemoattractants, by binding the receptor, inhibit CheA in E. coli (red line) (Borkovich et al. 1989) and stimulate CheA in B. subtilis (green line) (Garrity and Ordal 1997). CheA phosphorylates CheY. Phosphorylated CheY binds to the flagellar motor and increases the frequency of tumbles in E. coli (Cluzel et al. 2000) and runs in B. subtilis (Bischoff et al. 1993). Phosphorylated CheY is also predicted to inhibit the receptor complex in B. subtilis (dashed line). Both organisms tune the sensitivity of CheA to ligands by reversibly methylating the receptors using the CheR methytransferase and CheB methylesterase (Zimmer et al. 2000; Sourjik and Berg 2002b). Phosphorylation of CheB by CheA increases its methylesterase activity nearly 100-fold (Anand and Stock 2002). CheA activity is proportional to the degree of receptor methylation in E. coli. In B. subtilis, CheA activity depends on which residue is methylated, akin to a binary switch. E. coli possesses a phosphatase, CheZ, not present in B. subtilis, that enhances the rate of CheY dephosphorylation. B. subtilis possesses three chemotaxis proteins not found in E. coli: CheC, CheD, and CheV. CheC is a negative regulator of receptor methylation and homologous to the CheY-binding domain (P2) in CheA (Rosario et al. 1995; Rosario and Ordal 1996). CheD is a positive regulator of receptor methylation and also deamidates specific residues on the receptor (Kristich and Ordal 2002). CheV is a CheW-response regulator fusion. CheV is functionally redundant to CheW and is predicted to negatively regulate receptor activity (dashed line) (Rosario et al. 1994; Karatan et al. 2001).

So, yes, there are alternative ways in which different bacteria undergo chemotaxis, even with the same or similar components (for further information on the various chemotaxis systems, I refer readers to this paper). But having an alternative — even a simpler — means to accomplish a goal does not entail that you have a possible physical precursor which can be transformed step-by-Darwinian-step into the particular system which I described. The key defining characteristic of an irreducibly complex system is that multiple, co-ordinated and non-adaptive changes are required to attain novel utility. It is in achieving this end that the Darwinian mechanism is notoriously hopeless. As Michael Behe himself explains in response to John McDonald on the mousetrap

The second mousetrap (above) has a spring and a platform. One of the extended arms stands under tension at the very edge of the platform. The idea is that if a mouse in the vicinity jiggles the trap, the end of the arm slips over the edge and comes rushing down, and may pin the mouse’s paw or tail against the platform. Now, the first thing to notice is that the arms of the spring are in a different relationship to each other than in the first trap. To get to the configuration of the spring in the second trap from the configuration in the first, it seems to me one would have to proceed through the following steps[4]: (1) twist the arm that has one bend through about 90° so that the end segment is perpendicular to the axis of the spring and points toward the platform; (2) twist the other arm through about 180° so the first segment is pointing opposite to where it originally pointed (the exact value of the rotations depend on the lengths of the arms); (3) shorten one arm so that its length is less than the distance from the top of the platform to the floor (so that the end doesn’t first hit the floor before pinning the mouse). While the arms were being rotated and adjusted, the original one-piece trap would have lost function, and the second trap would not yet be working.

Moore also cites a 2009 paper by Schlesner et al. which concludes that “in the archael domain, previously unrecognized archaea-specific Che proteins are essential for relaying taxis signaling in the flagellar apparatus.” They also report,

Using protein-protein interaction analysis, we have identified three proteins in Halobacterium salinarum that interact with the chemotaxis (Che) proteins CheY, CheD, and CheC2, as well as the flagella accessory (Fla) proteins FlaCE and FlaD. Two of the proteins belong to the protein family DUF439, the third is a HEAT_PBS family protein. In-frame deletion strains for all three proteins were generated and analyzed as follows: a) photophobic responses were measured by a computer-based cell tracking system b) flagellar rotational bias was determined by dark-field microscopy, and c) chemotactic behavior was analyzed by a swarm plate assay. Strains deleted for the HEAT_PBS protein or one of the DUF439 proteins proved unable to switch the direction of flagellar rotation. In these mutants, flagella rotate only clockwise, resulting in exclusively forward swimming cells that are unable to respond to tactic signals. Deletion of the second DUF439 protein had only minimal effects. HEAT_PBS proteins could be identified in the chemotaxis gene regions of all motile haloarchaea sequenced so far, but not in those of other archaeal species. Genes coding for DUF439 proteins, however, were found to be integral parts of chemotaxis gene regions across the archaeal domain, and they were not detected in other genomic context.

So certain previously unrecognized Che proteins (which are specific to the archea domain) are essential for relaying chemotaxis signalling in archea. But the relevance of this to the present discussion is not entirely clear.

Moore also asserts that removing a single component rarely disrupts function. Contrary to this assertion, however, genetic knockout experiments reveal that knocking out single genes usually does disrupt function. As Rao et al. (2004) report,

E. coli and B. subtilis bias their motion towards favorable conditions with nearly identical behavior by adjusting the frequency of straight runs and reorienting tumbles. Both pathways (summarized in Figure 1 and Table 1) share five orthologous proteins with apparently identical biochemistry. How these individual orthologs contribute to the overall function, however, is different, as illustrated when synonymous orthologs are deleted in each organism. Deletion of the CheY response regulator causes E. coli to run exclusively and B. subtilis to tumble exclusively (Bischoff et al. 1993). When the CheR methyltransferase is deleted in E. coli, the cells are incapable of tumbles and only run. Likewise, when the CheB methylesterase is deleted, E. coli cells are incapable of runs and only tumble. In B. subtilis, cells still run and tumble when either CheB or CheR is deleted, though they no longer precisely adapt (Kirsch et al. 1993a, 1993b). Remarkably, both genes complement in the heterologous host. Deletion of the CheW adaptor protein in E. coli results in a run-only phenotype, whereas there is no change in phenotype for the synonymous deletion in B. subtilis. When the genes involved in regulating methylation are deleted (cheBR in E. coli and cheBCDR in B. subtilis), E. coli does not adapt (Segall et al. 1986), whereas B. subtilis either oscillates or partially adapts when exposed to attractants (Kirby et al. 1999). These differences demonstrate that the pathways are different even though they involve homologous proteins.

It seems that there are multiple systems, which could be argued to be irreducibly complex, in operation here. The CheY response regulator, for example, is an indispensable component, as illustrated in genetic knockout experiments where E. coli is seen to run exclusively and B. subtilis to tumble exclusively. Similar results are found when one knocks out the CheR methyltransferase in either E. coli or B. subtilis. CheW is indispensable to the system in E. coli, but not in B. subtilis. When you delete the genes involved in regulating methylation, the adaptation system in E. coli is completely lost, though only partially lost in B. subtilis.

Conclusion
I recommend that Dr. Moore re-read Michael Behe’s two books, Darwin’s Black Box and The Edge of Evolution for the ID perspective on the properties of irreducibly complex systems. Furthermore, I would stress once again that the case for design is not merely contingent on a negative complaint about the inadequacy of Darwinism. Rather, it is the observation that there are real engineering hallmarks in biological systems which forcefully compel the conclusion of intelligent design. Increasingly, we are learning that system evolvability requires the occurrence of multiple co-ordinated changes to facilitate novel utility and functional innovation. That is perhaps the biggest and most fundamental hurdle that the neo-Darwinian synthesis must overcome.

68 Replies to “YouTube’s “C0nc0rdance” Reassures Us That The Evolution Of Chemotaxis Is Well In Hand

  1. 1
    NickMatzke_UD says:

    CheW is indispensable to the system in E. coli, but not in B. subtilis. When you delete the genes involved in regulating methylation, the adaptation system in E. coli is completely lost, though only partially lost in B. subtilis.

    How can you admit such things and still take IC seriously as an argument? This is (a) direct evidence that “a knockout experiment shows this protein is essential in this one organism” doesn’t prove anything about other organisms, and (b) strong circumstantial support for the idea that parts can first be only helpful, and later become essential in some species, which indicates that “irreducible” does not equate with “unevolvable”.

    Knockout experiments are not equivalent to playing evolution in reverse — no more than cutting off someone’s head rewinds evolution to the time when heads were evolving and tell us it is impossible to gradually evolve a head. (for the record, head evolution was a very long and very gradual process starting with encephalization in wormlike ancestors, with skulls, jaws, necks, large brains, etc. all acquired sequentially much much later, and clearly traceable in detail in the fossil record).

  2. 2
    NickMatzke_UD says:

    Plus, like I said before, chemotaxis just ain’t that hard.

    ============
    Phys. Rev. Lett. » Volume 99 » Issue 17

    Phys. Rev. Lett. 99, 178103 (2007) [4 pages]
    Chemotaxis of Nonbiological Colloidal Rods

    Yiying Hong1, Nicole M. K. Blackman2, Nathaniel D. Kopp2, Ayusman Sen1,2,*, and Darrell Velegol2,3,*

    Received 21 June 2007; published 26 October 2007

    Chemotaxis is the movement of organisms toward or away from a chemical attractant or toxin by a biased random walk process. Here we describe the first experimental example of chemotaxis outside biological systems. Platinum-gold rods 2.0???m long exhibit directed movement toward higher hydrogen peroxide concentrations through “active diffusion.” Brownian dynamics simulations reveal that no “temporal sensing” algorithm, commonly attributed to bacteria, is necessary; rather, the observed chemotaxis can be explained by random walk physics in a gradient of the active diffusion coefficient.
    ============

    Moving over to biology, everything at the microscale has random movement due to Brownian motion random walks, anything that biases the random walk is chemotaxis of a sort already. The statement that “chemotaxis cannot evolve” is equivalent to saying that “no mutations will ever result in biased movement in a useful direction, when there are only two directions to choose from”.

    This is weak sauce for ID — go back to the structure of the flagellum, that was a bigger challenge.

  3. 3
    NickMatzke_UD says:

    (PS, I’m pretty sure it’s not the first known example, here’s another:

    Martin M. Hanczyc (2011). “Metabolism and motility in prebiotic structures.” Phil. Trans. R. Soc. B October 27, 2011 366:2885-2893; doi:10.1098/rstb.2011.0141

    2. Movement in a simple chemical system

    We have been studying the fundamental properties of movement in simple non-living systems based on an oil droplet in water [1–4]. When oil is mixed with water containing a surfactant, oil droplets spontaneously form. If a Marangoni instability occurs in the system, through either external manipulation or internal mechanism, the droplet interface will begin to move to resolve the instability. A Marangoni instability describes the flow of surfactant and liquid along an interface to equilibrate an imbalance in interfacial tension and is the underlying physical principle behind the ‘tears of wine’ effect. In a spherical oil droplet when a Marangoni instability occurs, both the interface and the internal volume can move forming a convective cell [5]. If convective flow is coupled with mass leaving the droplet from one pole as organized by the flow structures then the droplet can move through the aqueous environment. Through this purely physical mechanism, the droplet moves in order to preserve itself.

    Figure 1 shows a typical moving droplet experiment. Heavy nitrobenzene (NB) oil containing 0.5 M oleic anhydride and Oil Red O as colourant was placed in a glass-bottom disc containing both 10 mM oleate pH 12 micelles and a pH indicator, thymolphthalein. The pH indicator is blue at high pH and colourless below pH 11. As soon as the droplet was introduced to the water phase, it broke symmetry and began to move directionally around the dish (see electronic supplementary material, movie S1). As the droplet moved, it left a trail of low pH solution. This was expected owing to the encapsulated chemistry: the oleic anhydride upon exposure to water at the interface hydrolysed to form two oleic acid molecules. The production of acids at the oil–water interface can result in a local pH change of four units or greater [1]. This local change in pH was enough to change the interfacial tension around the droplet from 5 mN m?1 to nearly 25 mM m–1 [4]. Since the oil–water interface consisted of oleate/oleic acid with a pKa around 8.5, this local change in pH affected the state of the surfactant at the interface causing this shift in interfacial tension. An imbalance in interfacial tension was enough to initiate a Marangoni instability and fluid flow. When a convective cell was established inside the oil droplet, the droplet was able to move through the aqueous phase at speeds up to 1 cm s–1 and for more than 2 h, depending on the starting conditions. This droplet movement was sustained because the convective flow structure that initially forms to eliminate the imbalance in interfacial tension also introduces fresh anhydride from the inner oil phase to the interface where it was hydrolysed. Therefore, the imbalance in tension was maintained as long as there was precursor remaining in the droplet. The coupling of this simple one-step chemical reaction to the spherical oil droplet container formed a feedback loop that sustained a non-equilibrium mobile state over time.
    Figure 1.
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    Figure 1.

    Droplet moving in an aqueous pool containing surfactant. Droplet (red) was moving from the upper left to the lower right edge. The low pH trail was visualized by using the pH-sensitive dye thymolphthalein. Diameter of the section containing the aqueous pool was 27 mm.

    The droplet in this system was moving in response to its own self-generated pH gradient. We have also shown that the droplet was sensitive to externally applied pH gradients, with movement towards high pH. A droplet can sense pH gradients in its local environment and move towards high pH solution using its own particular form of chemotaxis [1]. As shown in figure 2, a droplet moving through the aqueous phase senses a pH gradient (blue), climbs the gradient and stops at the point of highest concentration (electronic supplementary material, movie S2). From such observations, we argued that the droplet has an interface that can sense its local chemical environment and an internal convective flow acting as a motor. Therefore, the system possesses a primitive form of sensory–motor coupling [4].
    Figure 2.
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    Figure 2.

    Chemotaxis of a droplet in a pH gradient. Each frame represents a 10 s interval. Droplet (red) was moving around aqueous pool until pH gradient was introduced in fourth frame. The dispersing pH gradient was visualized using the pH-sensitive dye, thymolphthalein. Diameter of the section containing the aqueous pool was 27 mm.

    We are interested in studying the emergence of life-like behaviours (like chemotaxis) in highly reduced and simple physico-chemical systems. The system above contains only five chemical components, including water. The emergent behaviour is due to the self-assembly of the oil molecules into a droplet, the exergonic imbedded hydrolysis reaction, an interface under tension, the flow and redistribution of surfactants along the interface owing to a physical instability initiated and maintained by the chemistry and finally movement primarily because of Newton’s third law with the product leaving the interface non-uniformly. All of this is coordinated by the convection flow that breaks the symmetry of the droplet and maintains a feedback loop coupling the chemistry to the physical motion. In principle, similar systems that share the basic characteristics of this system should also be capable of movement and perhaps chemotaxis. Therefore, we explored if such systems could represent a primitive form of life on the early Earth or elsewhere in the universe.

  4. 4
    ScottAndrews says:

    Nick,

    You’re stating the obvious to no apparent point.

    this is (a) direct evidence that “a knockout experiment shows this protein is essential in this one organism” doesn’t prove anything about other organisms

    Last I checked, I don’t rely on a flagellum or chemotaxis for mobility. Whether or not a component present in one organism is present in another has no bearing on the IC of that component.
    As was pointed out, being able to catch a mouse with glue or even live surrounded by mice is irrelevant to the IC of a mousetrap.

  5. 5
    Joseph says:

    For the record is there any genetic/ developmental evidence to support your imagination based on what you see in the fossil record?

    IOW Nick, how can we test your claim that head evolution was a very long and very gradual process starting with encephalization in wormlike ancestors, with skulls, jaws, necks, large brains, etc. all acquired sequentially much much later?

  6. 6
    Petrushka says:

    Similarly, it makes no sense to say that an automobile does not require an engine because one can use a bicycle! In like-manner, there are simpler ways to construct a flagellum. But that does not entail that a given flagellar system is not irreducibly complex.

    What does the term irreducibly complex mean in terms of evolvability if subcomponents are functional?

  7. 7
    Joseph says:

    Dr Behe responds:

    Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions

    And again it isn’t that the IC system didn’t evolve- if a targeted search is the mechanism then it can. The claim pertains to blind and undirected chemical, ie Darwinian, processes.

  8. 8
    ScottAndrews says:

    What does the term irreducibly complex mean in terms of evolvability if subcomponents are functional?

    It refers to the irreducible complexity of the component. If I take a lawnmower engine and hook it up to a generator (assuming that it’s a simple plug-and-play step) that doesn’t mean that converting to hand-crank generator to a gas-powered one is simple. See, you just co-opt a lawnmower engine. You still have to explain the lawnmower engine.

    And I’m making it sound simple. Every “co-option” story I’ve heard glosses over the details and just states that something took something and started using it for something else.

  9. 9
    NickMatzke_UD says:

    As was pointed out, being able to catch a mouse with glue or even live surrounded by mice is irrelevant to the IC of a mousetrap.

    Actually, considering that the Venus Flytrap evolved from a slowly-moving glue trap (which resembled Drosera, the sundew genus), which itself evolved from a non-moving glue trap (like Drosophyllum and other basal sticky-leaf trap carnivorous plants in the Drosersaceae), such facts are actually incredibly relevant, at least in actual biology.

  10. 10
    NickMatzke_UD says:

    Of course, in making this response, Behe abandoned the original logic for why IC was supposed to be a problem for evolution, which was that intermediate systems would be “by definition nonfunctional” and therefore wouldn’t have been preserved by selection.

  11. 11
    NickMatzke_UD says:

    IOW Nick, how can we test your claim that head evolution was a very long and very gradual process starting with encephalization in wormlike ancestors, with skulls, jaws, necks, large brains, etc. all acquired sequentially much much later?

    Start googling:

    Wormlike ancestors (and living relatives):

    Haikouella
    Yunnanozoon
    urochordates
    cephalochordates

    skulls, jawless fish:
    conodonts
    calcichordates
    lamprey
    hagfish

    jaws:
    placoderms
    cartilagenous fishes

    necks:
    Tiktaalik etc.
    http://en.wikipedia.org/wiki/T....._tetrapods

    big brains:
    http://pandasthumb.org/archive.....ini-1.html

  12. 12
    Petrushka says:

    Do you disagree that the inner ear bones are jaw bones used for something else?

  13. 13
    ScottAndrews says:

    Nick,

    I must admit, I thought you were running away from that subject (which would be the smart thing to do) since “actual biology” couldn’t even begin to detail the interrelated causes and effects that might produce such a transformation.

    But apparently now you have something substantial. My bad, I thought you were full of hot air, unable to distinguish your own speculation from ‘actual biological’ research, and trying to sound assertive because some people can’t tell the difference. I’m ready to stand corrected. Where’s the link?

  14. 14
    NickMatzke_UD says:

    This has nothing to do with me, I’m just telling you what is in the scientific literature, since you and many others are apparently happy to declare strong opinions without having looked any of this stuff up. The sticky leaf trap -> slow-moving sticky leaf trap –> fast-moving non-sticky leaf trap hypothesis was proposed by Darwin in his 1875 Insectivorous Plants and has since been confirmed by molecular, morphological, ecological, energetic, etc. studies.

    Molecular evidence for the common origin of snap-traps among carnivorous plants

    Kenneth M. Cameron2,4, Kenneth J. Wurdack5 and Richard W. Jobson2,3

    2The Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies, The New York Botanical Garden, Bronx, New York 10458 USA; 3Department of Botany, University of Queensland, Brisbane, Queensland 4072 Australia

    The snap-trap leaves of the aquatic waterwheel plant (Aldrovanda) resemble those of Venus’ flytrap (Dionaea), its distribution and habit are reminiscent of bladderworts (Utricularia), but it shares many reproductive characters with sundews (Drosera). Moreover, Aldrovanda has never been included in molecular phylogenetic studies, so it has been unclear whether snap-traps evolved only once or more than once among angiosperms. Using sequences from nuclear 18S and plastid rbcL, atpB, and matK genes, we show that Aldrovanda is sister to Dionaea, and this pair is sister to Drosera. Our results indicate that snap-traps are derived from flypaper-traps and have a common ancestry among flowering plants, despite the fact that this mechanism is used by both a terrestrial species and an aquatic one. Genetic and fossil evidence for the close relationship between these unique and threatened organisms indicate that carnivory evolved from a common ancestor within this caryophyllid clade at least 65 million years ago.

    Key Words: Aldrovanda * carnivorous plants * Dionaea * DNA * Droseraceae * molecular systematics * phylogeny

    Evolving Darwin’s ‘most wonderful’ plant: ecological steps to a snap-trap

    Thomas C. Gibson1,
    Donald M. Waller2

    Article first published online: 1 JUL 2009

    DOI: 10.1111/j.1469-8137.2009.02935.x

    New Phytologist

    Special Issue: Plant adaptation – following in Darwin’s footsteps

    Volume 183, Issue 3, pages 575-587, August 2009

    Summary

    Among carnivorous plants, Darwin was particularly fascinated by the speed and sensitivity of snap-traps in Dionaea and Aldrovanda. Recent molecular work confirms Darwin’s conjecture that these monotypic taxa are sister to Drosera, meaning that snap-traps evolved from a ‘flypaper’ trap. Transitions include tentacles being modified into trigger hairs and marginal ‘teeth’, the loss of sticky tentacles, depressed digestive glands, and rapid leaf movement. Pre-adaptations are known for all these traits in Drosera yet snap-traps only evolved once. We hypothesize that selection to catch and retain large insects favored the evolution of elongate leaves and snap-tentacles in Drosera and snap-traps. Although sticky traps efficiently capture small prey, they allow larger prey to escape and may lose nutrients. Dionaea’s snap-trap efficiently captures and processes larger prey providing higher, but variable, rewards. We develop a size-selective model and parametrize it with field data to demonstrate how selection to capture larger prey strongly favors snap-traps. As prey become larger, they also become rarer and gain the power to rip leaves, causing returns to larger snap-traps to plateau. We propose testing these hypotheses with specific field data and Darwin-like experiments. The complexity of snap-traps, competition with pitfall traps, and their association with ephemeral habitats all help to explain why this curious adaptation only evolved once.

    Energetics and the evolution of carnivorous plants–Darwin’s ‘most wonderful plants in the world’

    Aaron M. Ellison1,* and
    Nicholas J. Gotelli2

    + Author Affiliations

    1Harvard Forest, Harvard University, 324 North Main Street, Petersham, MA 01366, USA
    2Department of Biology, University of Vermont, 120 Marsh Life Sciences Building, Burlington, VT 05405, USA

    *To whom correspondence should be addressed. E-mail: aellison@fas.harvard.edu

    Received May 6, 2008.
    Revision received June 5, 2008.
    Accepted June 16, 2008.

    Carnivory has evolved independently at least six times in five angiosperm orders. In spite of these independent origins, there is a remarkable morphological convergence of carnivorous plant traps and physiological convergence of mechanisms for digesting and assimilating prey. These convergent traits have made carnivorous plants model systems for addressing questions in plant molecular genetics, physiology, and evolutionary ecology. New data show that carnivorous plant genera with morphologically complex traps have higher relative rates of gene substitutions than do those with simple sticky traps. This observation suggests two alternative mechanisms for the evolution and diversification of carnivorous plant lineages. The ‘energetics hypothesis’ posits rapid morphological evolution resulting from a few changes in regulatory genes responsible for meeting the high energetic demands of active traps. The ‘predictable prey capture hypothesis’ further posits that complex traps yield more predictable and frequent prey captures. To evaluate these hypotheses, available data on the tempo and mode of carnivorous plant evolution were reviewed; patterns of prey capture by carnivorous plants were analysed; and the energetic costs and benefits of botanical carnivory were re-evaluated. Collectively, the data are more supportive of the energetics hypothesis than the predictable prey capture hypothesis. The energetics hypothesis is consistent with a phenomenological cost-benefit model for the evolution of botanical carnivory, and also accounts for data suggesting that carnivorous plants have leaf construction costs and scaling relationships among leaf traits that are substantially different from those of non-carnivorous plants.

  15. 15
    Joseph says:

    Nick, I know the evidence. However there isn’t any evidence that changes in the genome can account for the physiological and anatomical transformations required.

    IOW Nick you need some genetic data to confirm the fossil data. Don’t ya think the tehory requires BIOLOGICAL data Nick?

  16. 16
    Joseph says:

    There isn’t any genetic evidence to support the claim that the Venus Flytrap evolved from a slowly-moving glue trap (which resembled Drosera, the sundew genus), which itself evolved from a non-moving glue trap (like Drosophyllum and other basal sticky-leaf trap carnivorous plants in the Drosersaceae),.

  17. 17
    Joseph says:

    Nick Matzke:

    Of course, in making this response, Behe abandoned the original logic for why IC was supposed to be a problem for evolution, which was that intermediate systems would be “by definition nonfunctional” and therefore wouldn’t have been preserved by selection.

    1- ID is NOT anti-evolution

    2- Behe said IC is a problem for blind and undirected chemical processes

    3- Your continued equivocation is duly noted

    4- If the intermediate systems have a DIFFERENT function then it is more of a problem for blind and undirected processes- duh

  18. 18
    Joseph says:

    There isn’t any evidence that jaw bones can become inner ear bones via blind and undirected chemical processes- well there isn’t any evidence that jaw bones can become inner ear bones.

  19. 19
    Petrushka says:

    ScottAndrews:

    Do you disagree that the inner ear bones are jaw bones used for something else?

  20. 20
    NickMatzke_UD says:

    Way to change the request! Now it’s “I require every mutation over 600 million years before I’ll believe the evolutionary position, whereas my ID position must provide absolutely no details of any kind whatsoever.”

  21. 21
    NickMatzke_UD says:

    Uh, you must have missed “Molecular evidence for the common origin of snap-traps among carnivorous plants” by Cameron et al. 2003. See the phylogeny with the characters mapped on.

  22. 22
  23. 23
    NickMatzke_UD says:

    Sure there is:

    http://www.talkorigins.org/faq.....diates_ex2

    The differences between these fossils are not large. Even young-earth creationists often accept that natural evolutionary processes can produce the differences that occur within genera and within families, these differences are on that level.

  24. 24
    Joseph says:

    Umm that evidence also points to a common design. Ya see no one has taken a slowly-moving glue trap, performed mutagenesis, and had a snap-trap develop.

  25. 25
    Joseph says:

    Umm that “evidence” assumes it happened, Nick. There isn’t any way to scientifically test the claim.

  26. 26
    Joseph says:

    The request is the same. YOU have failed to provide genetic evidence for your claim.

    Also ID is NOT anti-evolution.

    You have fossils but no way of determining how those fossils came to be.

    I used to be an evolutionist, Nick. That is until I started to peel away the curtains and found nothing but BS behind them.

  27. 27
    Joseph says:

    BTW there isn’t any evidence that a reptile can “evolve” into a mammal. The claim is untestable.

  28. 28
    Joseph says:

    There isn’t any evidence that mammalian middle ear bones were the jaw bones of reptiles.

  29. 29
    ScottAndrews says:

    Nick,

    Bluffing and condescension don’t answer this statement:

    “actual biology” couldn’t even begin to detail the interrelated causes and effects that might produce such a transformation

    You can document similarities and analyze prey capture all you want. The whole theory hinges on the part you keep avoiding.

    We’re talking about the supposed cornerstone of biology, and apparently you have no idea how it even works. The molecular similarities are interesting, but it’s the differences that require explanation. You’re taking a stab at why they are different but ignoring or assuming how. Did you think no one would notice?

    I think this is an accurate statement: Nick Matzke, the former Public Information Project Director at the National Center for Science Education, cannot even imagine how a series of selected genetic or regulatory variations might transform a flypaper trap into a snap-trap.

    It’s a bit harsh, but you like to throw rocks.

  30. 30
    Petrushka says:

    Do you disagree that a series of incremental steps can change jawbones into inner ear bones?

  31. 31
    ScottAndrews says:

    Petrushka,

    Ear bones are located near the jaw, so you could rightfully call them jaw bones used by the ears. But I don’t think that’s what you meant.

    You’re asking whether mammalian ear bones were once jaw bones that became used for a different function.

    I could answer it from an ID perspective – ID doesn’t have one. But you’re asking what I think personally.

    The evidence is sketchy. Evolutionists are fond of increasing their odds by claiming that there’s not just one target, that any given adaptation is one of many possible outcomes. Then they turn around and say that this very same ear evolution happened in multiple convergent cases. Given any number of possible outcomes it keeps hitting the same target.

    (It’s worth noting that the fossils used to support this transition aren’t even considered ancestors of mammals. They are a separate instance of the same thing supposedly happening.)

    That’s not an absolute logical contradiction, but it’s fishy.

    On top of that, even if one piece were modified to fit a different purpose, that doesn’t indicate natural selection at work because when you get down to the tiny details natural selection doesn’t explain such major changes. If the very same change is observed in several instances then design and reuse of components start making a lot more sense.

    I’m not trying to obscure your original question, but it’s a loaded one.

  32. 32
    ScottAndrews says:

    Petrushka,

    A series of incremental steps can change anything into anything.

  33. 33
    NickMatzke_UD says:

    Dude! If slow, gradual evolution happened in a well-fossilizable group, we should see a sequence of transitional fossils. And we do. Hypothesis proposed, hypothesis confirmed. This is how all science works. We didn’t see the Atlantic ocean open up through continental drift, but the cumulative case of confirming evidence is overwhelming.. Why do you want to treat evolution with rules different from those used for every other area of science?

    And, anyway, if you doubt that evolution happened between these forms, I guess you’re saying those highly similar fossils were each specially created, then went extinct — even though this makes you even more antievolutionary than a young-earth creationist who believes that evolution can happen within “kinds”? Where’s your evidence that this happened? Where’s your evidence that it is even possible? Are you just invoking dozens of miracles because you think it’s just impossible that evolution could move a few jawbones around a bit, which is the main difference between one transitional mammal-like reptile and the next one?

  34. 34
    Joseph says:

    Dude, the design inference is based on our knowledge of cause and effect relationships in accordance with uniformitarianism- so why do YOU want to treat ID with rules different from those used in every other area of science? Well except for your position which remains untestable.

    Let me remind Nick that ID is not anti-evolution and evidence for common descent is not evidence for any mechanism.

    Also I will remind Nick the overwhelming majority of fossils of of marine invertebrates and in that vast majority we do not see evidence of universal common descent.

    That said, Nick, all I am asking for is something, anything that demonstrates the transformations required are even possible via changes to the genome.

    And just how are YOU defining evolution?

  35. 35
    Petrushka says:

    The question I asked isn’t even about mechanism. I asked whether jawbones can change incrementally into inner ear bones. Feel free to invoke a Designer to make the changes, one by one if you think that’s how it happened.

    And feel free to explain the sequence of changes if they occurred somewhere than in the genome.

  36. 36
    Petrushka says:

    My question isn’t really about mechanism. It’s whether jaw bones can be modified incrementally to make inner ear bones. Feel free to attribute the incremental changes to a designer.

    Is the incremental change possible?

  37. 37
    ScottAndrews says:

    I’ll say yes. Just about anything can be modified into just about anything else through incremental steps. Bones are no exception.
    Unless you mean something more specific by incremental. The term could be applied to anything. When I type add letters to words and words to sentences.

  38. 38
    Petrushka says:

    I’m not trying to be devious. Regardless of whether the specific fossil record shows ancestors or cousins, it shows a transition fro jaw bones to inner ear bones. It shows the incremental transition from one function to a new and complex function.

    I have trouble understanding how the best possible explanation of the transition is design.

    Jaw bones are very malleable and easily subject to selection. Look at what we’ve done with dogs in just a few hundred years.

    So in my mind the argument boils down to the attributes of the landscape, and whether research will demonstrate that the functional landscape supports incremental phenotypical change.

    This is developmental stuff, not the hard stuff that Behe writes about, like the origin of protein families.

  39. 39
    ScottAndrews says:

    Petrushka,

    I don’t think you’re trying to be devious. I’m just being careful about what I agree with.

    Regardless of whether the specific fossil record shows ancestors or cousins, it shows a transition fro jaw bones to inner ear bones. It shows the incremental transition from one function to a new and complex function.

    This is incorrect in a very significant way. The increments of darwinian change are genetic, and you can’t derive those genetic differences from fossils. The increments you’re referring to are fuzzier. This looks like that, this is a little different, etc.

    In a sense, comparing one of these bones to another is like comparing a sparrow to a hummingbird. It’s one thing to observe a similarity. But lining up similar things to show a transition does not explain the transition. This is so even if the transition did take place.

    At present there is no plausible explanation for such a transition occurring naturally. That transition would have to consist of an accumulation of individual genetic variations such as has never been observed or even hypothesized.

    For that reason and others I question the transition itself. There’s too much wrong with the picture.

    But that’s secondary. My primary point is there is no biological explanation for that variation or any other such significant differences. It’s widely spoken of as if it’s settled, but there’s literally nothing there.

  40. 40
    Petrushka says:

    At present there is no plausible explanation for such a transition occurring naturally. That transition would have to consist of an accumulation of individual genetic variations such as has never been observed or even hypothesized.

    Well try to stick around another 50 years. I don’t know if we can reconstruct dinosaurs, but we are beginning to reconstruct transitionals at the genetic level. At the moment this is limited to a few mutations in bacteria, but new technologies have to start somewhere.

    Do you really doubt that selective breeding doesn’t accumulate genetic differences?

  41. 41
    ScottAndrews says:

    Petrushka,

    Selective breeding results in genetic differences, greater than if the breeding were not selective.
    But as far as we know you can’t breed lizards and get mammalian ears. Not even if you repeatedly select the ones with the best hearing and have lifetimes to try.
    I’m not saying it’s impossible, but there’s nothing to support it. Similar experiments on bacteria haven’t turned up anything notable.

    As for the next 50 years, anyone is free to pick a horse and be optimistic. But I really hope that all those experiments aren’t carried out by people who have already decided what they expect to find. That would be a waste of 50 years.

  42. 42
    Petrushka says:

    But as far as we know you can’t breed lizards and get mammalian ears. Not even if you repeatedly select the ones with the best hearing and have lifetimes to try.

    But that line of reasoning supports common descent, because evolution can’t go sideways. It always has to vary incrementally from what it’s got right now.

    That’s why you get extinctions. Perfect adaptation can be a perfect blind alley, from which there is no avenue to adapt to large changes in climate or conditions.

    Designers, on the other hand, can move genes from plants to animals and vice versa. Which is how genetic engineering could be detected, even if humans disappear from the earth.

  43. 43
    Joseph says:

    My point is there isn’t any evidence the changes were due to changes in the genome. There isn’t any evidence that organisms are a sum of their genome.

    But anyway, yes, the only way jaw bones could possibly become inner ear bones is by design – IMO.

  44. 44
    Joseph says:

    Petrusghka:

    But that line of reasoning supports common descent, because evolution can’t go sideways.

    It goes any way the surviving reproducers take it. And from all observation that is a wobbling stability

    And then we have:

    Can evolution make things less complicated?

    Instead, the data suggest that eukaryote cells with all their bells and whistles are probably as ancient as bacteria and archaea, and may have even appeared first, with bacteria and archaea appearing later as stripped-down versions of eukaryotes, according to David Penny, a molecular biologist at Massey University in New Zealand.

    Penny, who worked on the research with Chuck Kurland of Sweden’s Lund University and Massey University’s L.J. Collins, acknowledged that the results might come as a surprise.

    “We do think there is a tendency to look at evolution as progressive,” he said. “We prefer to think of evolution as backwards, sideways, and occasionally forward.”

  45. 45
    Petrushka says:

    We’re not discussing stability, but a specific case of the evolution of a complex new function, incrementally, by modifying parts used for a previous function.

    It happened. You can assert it was the work of a designer if you want, but the incremental change occurred.

  46. 46
    ScottAndrews says:

    Petrushka,

    If you bred lizards and only kept the ones with the best hearing, it should be functionally the same as natural selection, except far more specific. Genetic engineering moves genes around. It doesn’t depend strictly on heredity and selection.

    It’s claimed that mammalian ears have evolved convergently several times, so now the expectation is created that similar results might occur again. Unless convergent evolution is just another convenient story.

    Designers, on the other hand, can move genes from plants to animals and vice versa. Which is how genetic engineering could be detected

    I don’t know. We see lots of stuff that appears to be engineered with no other explanation, and that gets shrugged off pretty easily. I don’t expect that more evidence would get received very differently unless people clear away the cobwebs first.

  47. 47
    NickMatzke_UD says:

    I think this is an accurate statement: Nick Matzke, the former Public Information Project Director at the National Center for Science Education, cannot even imagine how a series of selected genetic or regulatory variations might transform a flypaper trap into a snap-trap.

    It’s a bit harsh, but you like to throw rocks.

    Oh please. Do you really believe that it’s unlikely that regulatory mutations can turn up or turn down the level of mucilage secretion on a leaf?

    Do you really believe that it’s unlikely that regulatory mutations can make a leaf a bit convex, such that when the usual “slow” Drosera-type movement starts in Dionaea, it leads the leaf to mechanically “pop” from convex to concave.

    I’ve already won this argument, although you might not realize it yet.

    I’ve explained how the big changes happened, such that you yourself are now reduced to arguing about the small changes, which are actually quite trivial quantitative changes in continuous traits, just the kinds of things that are easy to understand as the product of slight mutational modifications in binding sites, which lead to slight changes in expression.

  48. 48
    Petrushka says:

    Ten years ago we couldn’t compare whole genomes. Now we have a thousand or so, mostly microbes.

    A lot of our arguments are futile and cannot be resolved without access to the data. Which is coming. It’s like we suddenly went from hand held magnifiers to scanning electron microscopes.

    There’s a fossil record in genomes.

  49. 49
    NickMatzke_UD says:

    Umm that evidence also points to a common design.

    The common design proposal/random desperate response IDist fling out when they can’t think of anything else is code for “GodDidIt but for some reason he made it look like evolution, I’m invoking God’s all-powerful miracle in order to avoid a conclusion I don’t like, because I don’t have any actual evidence against the evolutionary conclusion.” This is on the same level as the appearance-of-age stuff that the YECs do.

    Ya see no one has taken a slowly-moving glue trap, performed mutagenesis, and had a snap-trap develop.

    No one has ever split a continent in a lab either. This is not evidence against continental drift. The number of scientific topics on which lab experiments are possible / fundable / short-enough-to-produce-results-in-a-year-or-two is very small compared to the number of topics science successfully explores.

    Besides, even the young-earthers accept within-genus evolution, and snapping ability has evolved even within the genus Drosera.

  50. 50
    NickMatzke_UD says:

    Also I will remind Nick the overwhelming majority of fossils of of marine invertebrates and in that vast majority we do not see evidence of universal common descent.

    You got this from the weird mind of Phillip Johnson, it ain’t actually true.

    That said, Nick, all I am asking for is something, anything that demonstrates the transformations required are even possible via changes to the genome.

    The differences in these skulls aren’t obviously bigger than the differences in the skulls of different dog breeds.

  51. 51
    ScottAndrews says:

    Petrushka,

    You’re still using the term ‘incremental’ incorrectly.

    a specific case of the evolution of a complex new function, incrementally, by modifying parts used for a previous function.

    If we allow that a transition took place, we still do not see incremental change. Increments are genetic.

    I don’t mean to by cynical, but people have been playing fast and loose with the evidence in general and fossils in particular for years. Paleontology just doesn’t have the same credibility as other sciences because they have a way of extrapolating what they want to see and then brushing it under the table when something better comes along. If mammalian ear transitions were as cool as ape-men then new mammalian ear transitions would be growing on trees.

    If there were any detailed evidence or even hypotheses regarding the individual variations and selections in this or any other case then that would lend some credibility to the fossils. No matter where you poke it it’s soft and squishy.

  52. 52
    Joseph says:


    Also I will remind Nick the overwhelming majority of fossils of of marine invertebrates and in that vast majority we do not see evidence of universal common descent.

    Nick Matzke:

    You got this from the weird mind of Phillip Johnson, it ain’t actually true.

    Actually I got it from research and it is true. It is also pretty much expected given what we know of the fossilization process.

    Not Philip Johnson-Exposing the Evolutionist’s Sleight-of-Hand With the Fossil Record

    That said, Nick, all I am asking for is something, anything that demonstrates the transformations required are even possible via changes to the genome.

    The differences in these skulls aren’t obviously bigger than the differences in the skulls of different dog breeds.

    I am unaware of any dog breeds that had their inner ear bone become jaw bones. Nor have any dog breeds become retiles.

    IOW it appears there is a limit to the variation.

  53. 53
    Joseph says:

    Nick matzke:

    The common design proposal/random desperate response IDist fling out when they can’t think of anything else…

    That’s just plain ole ognorant. The common design argument is based on observation and experience- we have communication standards and building codes and safety regulations- all of this leads to a commonality amongst interacting systems and components. IEEE- ever hear of them?

    Also ID is not anti-evolution and it only “looks like the blind watchmaker didit” to those who cannot afford to say anything else.


    Ya see no one has taken a slowly-moving glue trap, performed mutagenesis, and had a snap-trap develop.

    No one has ever split a continent in a lab either.

    We have modeled plate tectonics- we did this because we understand ALL of the processes involved. OTOH developmental biology hasn’t helped you. All you can do is say “it looks like the blind watcghmaker didit to me”.

    Also “Genus” is an artificial construct.

    But anyway all I am doing is looking for a way to scientifically test your claims. If all you can do is throw father time around, as if that solves your problems, proves you have no interest in science.

    Cause and effect- we need a viable cause to produce the effect you speak of. And then we need to be able to test that cause to see if it is up to the task.

    Other than that all you have are theoretical musings of past events. Nice for novels but not good enough for science.

  54. 54
    NickMatzke_UD says:

    Actually I got it from research and it is true. It is also pretty much expected given what we know of the fossilization process.

    Not Philip Johnson-Exposing the Evolutionist’s Sleight-of-Hand With the Fossil Record

    OK, well, Phillip Johnson said it years before this guys essay/wildly inaccurate screed was published.

    There are lots of transitional fossils, both for invertebrate groups, and for the origin of vertebrate from invertebrates (which your link says don’t exist, but which we already briefly showed in this thread).

    Read this book:

    Prothero (2007). Evolution: What the fossils say and why it matters.

    That said, Nick, all I am asking for is something, anything that demonstrates the transformations required are even possible via changes to the genome.

    The fossils show that the necessary changes were small and gradual. Basically they are changes in the size and position of different bones. Some of the accessory jawbones at the back get reduced in size and eventually become so small they retain only a sound-transmission function (which was originally a function for several jawbones).

    I am unaware of any dog breeds that had their inner ear bone become jaw bones. Nor have any dog breeds become retiles.

    IOW it appears there is a limit to the variation.

    You’re just saying that because someone has told you that dog variation is “just” within-species variation. When they do morphometric analyses, it turns out that the variation in dog skulls is on the same order of variation in the skulls of order carnivora. It’s “intraspecific macroevolution”.

    http://pandasthumb.org/archive.....fic-m.html

    If someone handed you the fossils out of the blue, and you’d never heard of dogs, you’d say the differences between a chihuahua and a bulldog were bigger than the differences between two close cousins in the mammal stem-group (I called those reptiles earlier, modern terminology actually dispenses with the “reptile” terminology, since really, these fossil things are closer to living mammals rather than living reptiles, and yet do not fall within living mammals. Thus they are on the mammal stem.)

  55. 55
    ScottAndrews says:

    You too, Nick?

    The fossils show that the necessary changes were small and gradual.

    I’d love to hear how you divine individual genetic variations from fossils. Like everything you guys say, it sounds reasonable as long as you stay away from details. If you can convince people that you saw genetic variation and selection in the fossil record you can tell them anything.

    I think that’s why you drop in occasionally to insult everyone. Most people believe everything you say, and it irks you that the only people who critically analyze any of it dismiss it.

  56. 56
    NickMatzke_UD says:

    It’s claimed that mammalian ears have evolved convergently several times, so now the expectation is created that similar results might occur again.

    Sometimes it sounds like this in press reports and less-than precise language that some (usually older) researchers use, and if you use the old single-character definition of mammals and use linking of the 3 middle-earbones in the classical mammalian fashion as The One True Definition of mammals then this even translates into “mammals evolved several times”. But what is actually going on is that on the stem leading to mammals, up near the top of the stem below the mammal crown, you have a bunch of not-quite-crown mammals that all have ear/jawbone configurations that are close to, but not quite at, the mammalian configuration. Then you have a bunch of early mammals that share a bunch of characters with the not-quite mammals.

    These things are all fairly close relatives, and this means that the details of the inferred relationships can change somewhat depending on the analysis method, which critters are included, etc., even though all of them fall out pretty close to each other in the grand phylogenetic scheme of things. And sometimes the result is observed that it looks like the final step or two of middle-ear evolution happened more than once. This actually is not all that unlikely, since the starting points for these “independent acquisitions of the mammalian middle ear” are all almost-mammals already and all start with almost-mammalian-middle ear. Could the three bones have gone from almost-linked to linked twice instead of once? Sure. However, saying this is a very long ways from the statement that the mammalian middle ear evolved convergently multiple times completely from scratch.

  57. 57
    NickMatzke_UD says:

    I don’t mean to by cynical, but people have been playing fast and loose with the evidence in general and fossils in particular for years. Paleontology just doesn’t have the same credibility as other sciences because they have a way of extrapolating what they want to see and then brushing it under the table when something better comes along. If mammalian ear transitions were as cool as ape-men then new mammalian ear transitions would be growing on trees.

    That’s just silly. You should sit through a comparative anatomy class and a vertebrate morphology class, memorize the names of a few thousand skeletal features and their distribution across vertebrates, throw in several geology courses, especially sedimentology and stratigraphy, add in several summers worth of field camps, then publish a few fossil descriptions, and then reassess your statement.

  58. 58
    Joseph says:

    Comparative anatomy- convergence and common design

    Vertebrate morphology- convergence and common design

    The point being is that universal common descent is not the only explanation for these.

  59. 59
    Joseph says:

    Niick:

    OK, well, Phillip Johnson said it years before this guys essay/wildly inaccurate screed was published.

    Just saying it’s inaccurate doesn’t make it so.

    There are lots of transitional fossils, both for invertebrate groups, and for the origin of vertebrate from invertebrates (which your link says don’t exist, but which we already briefly showed in this thread).

    The “transitionals” for inverts was taken care of in that article.

    Transitions from invert to vert? Where?


    That said, Nick, all I am asking for is something, anything that demonstrates the transformations required are even possible via changes to the genome.

    The fossils show that the necessary changes were small and gradual.

    Maybe in your imagination they do, but you still need some biological evidence to support your imagination.


    I am unaware of any dog breeds that had their inner ear bone become jaw bones. Nor have any dog breeds become retiles.

    IOW it appears there is a limit to the variation.

    You’re just saying that because someone has told you that dog variation is “just” within-species variation.

    It is, no one had to tell me. And all observations and experiments say there is a limit.

    When they do morphometric analyses, it turns out that the variation in dog skulls is on the same order of variation in the skulls of order carnivora.

    No ear bones from jaw bones- nothing tat even makes the breeds different species.

    You are fibbing.

    If someone handed you the fossils out of the blue, and you’d never heard of dogs, you’d say the differences between a chihuahua and a bulldog were bigger than the differences between two close cousins in the mammal stem-group

    That blows your reliance on the fossil record out of the water!

    You have proven that looking at fossils is subjective.

    Thank you.

  60. 60
    Joseph says:

    There still isn’t any way to test the claim that a population of repriles evolved into a population of mammals.

    There isn’t any genetic evidence to support the alleged transition.

    The theory of evolution is a BIOLOGICAL theory and as such requires biological evidence to support it. So it is strange taht said biological evidence is no where to be found.

  61. 61

    It’s not the only possible explanation, but it is an extremely well supported explanation, accept by a great many ID proponents among others.

  62. 62
    Joseph says:

    Except it isn’t supported. How can it be there isn’t any way to scientifically test the claim?

    Methinks you are confused…

  63. 63
    NickMatzke_UD says:

    Except it isn’t supported. How can it be there isn’t any way to scientifically test the claim?

    Methinks you are confused…

    …and…

    There still isn’t any way to test the claim that a population of repriles evolved into a population of mammals.

    There isn’t any genetic evidence to support the alleged transition.

    The theory of evolution is a BIOLOGICAL theory and as such requires biological evidence to support it. So it is strange taht said biological evidence is no where to be found.

    Dude! You might as well make that argument about DNA evidence in court, because it’s the same dang evidence.

    Biological reproduction means DNA is passed from parent to offspring with a small number of mutations.

    This means that children will be similar to parents, both in the DNA sequence and in their overall morphology.

    This similarity will gradually decrease as the number of generations increases.

    This means closer relatives will have more similar DNA than more distance relatives.

    This is what we observe when we look at the DNA of vertebrates. Mammals are sister to reptiles. Birds are a subgroup of reptiles.

    The exact same logic (and sequencing methods and statistical software!) has been used, in court, to trace transmission of HIV from carrier to victims.

    It’s used when the US Fish and Wildlife Department confiscates illegally imported plant and animal products that they can’t identify — they get the DNA, they find out whether it is from an endangered species, etc.

    The same logic is used whenever people due paternity tests, identify a criminal by finding his brother in the DNA databases, etc.

    What would happen if you walked into court in any of these cases and said “Oh, this stuff is all invalid, because it could have been common design, where God’s miraculous miracle power was used to poof these similar DNA sequences into existence and for some reason He decided to make it look exactly like it would look if the DNA pattern had been repoduced by the physical relationship of copying from parent to child.” Good luck with that!

    “Common design” is no better than “appearance of age”. Go read Omphalos.

  64. 64
    Petrushka says:

    If we allow that a transition took place, we still do not see incremental change. Increments are genetic.

    Are you suggesting that incremental changes in phenotype don’t reflect underlying changes in genotype? I’m having trouble understanding your point.

  65. 65
    ScottAndrews says:

    Petrushka,

    Of course changes in phenotype reflect underlying changes in genotype. That’s the point. Evolutionary changes are genetic. But when you compare two fossils and determine that they have changed incrementally, what is the underlying genetic change?
    It’s one thing that you can’t identify a change. It’s another that you can’t tell whether it was a single genetic change, or two, or a dozen.
    Evolution is based on incremental genetic changes, and you cannot read them from the fossil record. When you say “incremental changes” in the fossil record, you’re not referring to the same incremental changes that define evolution.

  66. 66
    ScottAndrews says:

    And from there it follows that you cannot use the fossil record to support the hypothesis that a single genetic variation occurred, and was selected, followed by another variation, etc. You cannot use the fossil record to support natural selection operating on variation. All you can do is observe what may or may not be a transition and wonder what happened.

  67. 67
    ScottAndrews says:

    Nick,

    In a court of law, there’s a simple explanation for passing DNA from person to person or from plant to plant.

    I’d love to ask in that same court how DNA from a sea cucumber got into a person. Or how a common ancestor passed DNA to both a lizard and a horse. I know you could explain, but only as long as it stayed high-level and vague. The devil is in the details and the accused would be acquitted.

  68. 68
    knethrea says:

    All this arguing and DI’s best is still god of the gap/argument from ignorance. ID is not a valid hypothesis. Hypothesis needs to be built on things we can demonstrate exist. Don’t need all these details until you can get a designer to respond under control. ID explains nothing.

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