New Limbs from Old Fins, Part 6

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October 20, 2011 Tags: History of Life

Today's entry was written by Stephen Matheson. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

In this series, we have looked at the evidence that has led biologists to conclude that the limbs of animals like birds, bats, and brachiosaurs have their historical roots in the fins of fish. We explored shared anatomical features, fossils of extinct transitional forms, conserved cellular signaling systems, and homology in genetic systems, and we discussed these data in the context of the concept of homology. Common descent, I have argued, provides a coherent and unified explanation for these observations. In fact, by looking at data of very different kinds, we have seen two major strengths of evolutionary theory – its explanatory power and its fruitfulness across various scientific disciplines. There is no competing scientific explanation, at least not today.

We will conclude our series by addressing two interesting questions that have come up along the way and by looking closely at the meaning of purpose and design in the context of evolutionary explanation.

Not just homology. Deep homology.

In the previous post, we saw that genetic control systems involved in the development of fish fins and animal limbs are strikingly similar, so much so that genetic switches can be transplanted among organisms as different as fish, birds, and mammals. Observations like those strengthen the conclusion that chick wings, mouse paws, and (amazingly) fish fins are homologous, meaning that they are altered versions of a common ancestor. Chick wings and mouse paws are classic examples of structures that display homology.

There are, however, zillions of other animals with legs. It's hard to think of an animal that doesn't have appendages of some kind. What about all those other legs? Are they all homologous to each other? Specifically, are the legs of insects somehow homologous to the limbs of mice? (I'll focus on insects here, but the same conclusions apply to all arthropods.)

The answer is: almost certainly not. For one thing, there are few structural similarities. More importantly, a look at the animal family tree shows that there are animals "between" insects and tetrapods that don't have structures comparable to either limbs or insect legs. In other words, fins and insect legs each developed in different organisms, who originally had no appendages at all. The two branches arose independently, as near as we can tell, and so fly legs and mouse paws are not homologous.

But, shockingly, the genetic systems that control their growth are strikingly similar. Fly leg development is controlled by Hox genes. More amazingly, fly leg development is controlled by many of the same Hox genes that perform similar tasks in mice. Fly legs are not homologous to mouse paws, but it looks like the genetic systems that control their development are, to a large extent, homologous. Neil Shubin, Cliff Tabin, and Sean Carroll coined the term 'deep homology' to describe this phenomenon in the influential 1997 article "Fossils, genes and the evolution of animals limbs". Deep homology, then, refers to historical continuity of genetic control systems that underlie patterns or forms that are not so evidently homologous—like fly legs and mouse paws.

Deep homology has been seen in other developmental contexts. One of the more famous examples is the development of the eye or, more accurately, the development of eyes. Eyes are wildly different in different kinds of animals (consider the camera-like human eye compared to the compound eye of a fly), and they develop in very different ways in different kinds of animals. They seem not to be homologous; on the contrary, they seem to have evolved independently dozens of times. But a look under the hood shows remarkable deep homology – the genetic control systems are homologous. In one of the most dramatic experiments in developmental genetics, scientists in Walter Gehring's lab in Germany were able to induce the growth of extra eyes in fruit flies, by flipping a genetic switch, and it didn't matter whether the switch came from a fly or from a mouse. The mouse switch could turn on eye development in a fly. The picture below shows a fly with eyes growing on all six of its legs! (The eyes are the reddish-brown blobs on the legs, which are on the left side of the photo.)

Deep homology has important implications for our understanding of the development of life on earth, and its discovery helped trigger the birth of a new branch of biology, a sort of hybrid of evolutionary biology and developmental biology: evolutionary developmental biology, or evo-devo. The fins-to-limbs story is an exemplar of evo-devo thought, which emphasizes the role of conserved genetic control systems in the development of the magnificent diversity of animal forms. The basic idea is that these ancient genetic control systems make excellent "toolkits" that can be modified extensively to generate those seemingly endless "variations on a theme" that fins and limbs exemplify so beautifully. Fly legs and human arms may not be structural homologs, but the deep homology in their genetic underpinnings suggests that they are variations on a theme – perhaps we can call it the "outgrowths" theme – that was established in some of the most ancient animals of all.

Tetrapods without limbs?

We saw in the first post that snakes and whales are classified as tetrapods, even though neither has four limbs. What's up with that?

The simplest explanation is this: snakes and whales are classified as tetrapods because they are descended from tetrapods. To a biologist interested in classification, the term 'tetrapod' refers to a group of organisms related by descent, and not necessarily to a group of organisms that have a particular set of features. This is more common than you might think. For example, there are flies that have neither wings nor legs, but are still classified as flies (and as insects). Darwin himself, in the Origin of Species, wrote that "all true classification is genealogical," meaning that life is best understood as a "community of descent." So, snakes and whales are animals with less than four limbs that have descended from animals with four limbs.

Why do biologists think that snakes are descended from card-carrying tetrapods? The evidence they rely on is the same kind of evidence that we looked at throughout this series: shared anatomical features, fossil intermediates, conserved developmental and genetic toolkits. Consider, for example, the pelvic girdle (the part of the skeleton to which the legs attach) of a tetrapod. Some snakes (like pythons) still have that pelvic girdle, and those snakes grow tiny limb buds. Fossil snakes with tiny (and shrinking) hindlimbs have been clearly described. What about the genetic toolkit? It's conserved, with some changes that inactivate the limb-growing signal at just the right time. We know the signal is there because a limb bud from a python can cause limb growth in a chicken! Snakes, it seems, are elongated tetrapods with reduced (or erased) leg development.

The natural history of whales is better known thanks to some truly spectacular fossil intermediates discovered in the last 20 years or so. That story has been nicely covered previously on this blog, and the outline is familiar: common anatomical themes, striking fossil intermediates, and genetic data all point to a land-dwelling tetrapod mammal as the common ancestor of all whales (including dolphins). We can "watch" the hindlimbs disappear in a historical sketch based on fossils, and we can see what happens when the hindlimb-making program is accidentally turned back on. As you might have guessed, that rare event results in a dolphin with vestigial hindlimbs, arising from seemingly normal limb buds that occur in every dolphin embryo. Dolphins, it seems, are streamlined tetrapods with reduced (or erased) hindlimb development.

Descent versus design

The natural history of tetrapods is a superb example of the explanatory power of common ancestry. Each line of evidence – anatomy, fossils, developmental mechanisms, shared genetic toolkits – is interesting and suggestive. But taken together, the data form a distinctive body of observations that are convincingly explained by common descent. No competing explanation comes close.

Design, of course, is one proposed explanation for some of the data we've examined. As a competing explanation, design is currently a failure. Whether we look at structural themes or underlying genetic systems, we can identify no clearly-defined principles of functional optimization. In other words, we have no good reason to suppose that the tetrapod limb blueprint (one bone, two bones, blobs, digits) represents the only way – or even the best way – to build a limb (or a wing or a flipper). We have no good reason to suppose that Hox genes are the only way – or the best way – to turn on gene expression systems underlying limb development. We have no good reason to suppose that the Sonic Hedgehog protein is the only way – or even the best way – to send growth signals through a limb bud (or a fin bud). In each of those cases, we have no good reason to suppose that it could not have been otherwise, and in some cases, we know that it can work in other ways.

Design does not help us make sense of the patterns in the fossil record as exemplified by animals like Tiktaalik. Design does not help us make sense of the temporary hindlimbs of embryonic dolphins, nor does it account for deep homology. Design, to whatever extent it stands for functional optimization or even excellence, is unhelpful as an explanation when it comes to limbs and fins and their shared characteristics.

This could change, of course. Scientists may learn that there are yet-unknown design constraints that dictate one or a very few optimal configurations for limb and fin construction, such that things really could not have been otherwise. (Perhaps those scientists who prefer design-based explanation will take the lead on this one.) In fact, I argue that the only way to establish design as a competing explanation, one that can rival the explanatory power of common descent, is to convincingly demonstrate something akin to a set of profound biological design constraints. To unseat common ancestry, or at least to rival it, design theory has to show that life could not have been otherwise.

Descent with design

But design need not compete with common ancestry. Some design theorists do in fact accept common descent, and seek to identify marks of design in the processes by which the tree of life came to be. These attempts vary in quality, and the better-known examples have been discussed on this blog in detail. The point is that design thought, whether it posits supernatural "intervention" or mulls "front-loading," need not be inherently dismissive of the explanatory power of common ancestry.

In fact, I think some emphasis on design is important to retain while considering evolution. For Christians, one reason for this is simply the fact that we confess the biological world to be the creation of the Creator God. There's also another more subtle reason: design in some form may be a necessary explanatory principle. One point at which design and descent seem confluent is in the ideas and emphases of paleontologist Simon Conway Morris. Recently discussed on this blog, and now in a complete web site, Conway Morris' theme is evolutionary convergence – the striking tendency of evolution to repeatedly "discover" design themes. Perhaps ideas like his are pointing us to principles of design and purpose that run deep in the living world, or perhaps they simply tell us a bit more about how God's world really works.

Further Reading

Neil Shubin (2009) Your Inner Fish: A Journey Into the 3.5-Billion-Year History of the Human Body. New York: Vintage Books.

Brian K. Hall, editor (2007) Fins into Limbs. Chicago: The University of Chicago Press.

John Gerhart and Marc Kirschner (1997) Cells, Embryos, and Evolution. Malden (MA): Blackwell Scientific.

Neil Shubin, Cliff Tabin and Sean Carroll (2009) Deep homology and the origins of evolutionary novelty. Nature 457:818-823.

Sean B. Carroll (2005) Endless Forms Most Beautiful: The New Science of Evo Devo. New York: W.W. Norton & Co.

Sean B. Carroll (2008) Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution. Cell 134:25-36.

Image credit:

Figure 2C of Gehring. (2011) Genome Biology and Evolution 3:1053-1066.

Stephen Matheson is an author, editor, and developmental cell biologist, formerly at Calvin College in Grand Rapids, Michigan. He writes regularly on his blog “Quintessence of Dust”, which explores issues of science and Christian faith, focusing on genetics, development, evolution, neuroscience, and related topics, regularly discussing intelligent design, creationism, and other scientific issues that worry evangelical Christians.

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mjblyth - #65633

October 20th 2011

If the common ancestor of vertebrates and arthropods did not have “legs,” but they both now have legs whose development is controlled by homologous genes or genetic systems, how did that come about? What were those systems doing in the common ancestor if not something limb-related? Do the limbless animals also still have the same homologs, and is their function known? I’m sure no one thinks it was just a coincidence that the same Hox genes were used to control limb development twice.

sfmatheson - #65639

October 20th 2011

So, one hypothesis is that the whole thing is a “coincidence.” Or, more technically, a stunning example of convergence. Seems nearly impossible, at least to me. Here’s how Shubin, Tabin, and Carroll explain the alternative hypothesis, in the 1997 paper:

“The second model is that some of these genes or circuits were components of an ancestral genetic regulatory system that was used to pattern a structure in the common ancestor of vertebrates and arthropods. This ancestral structure need not have been homologous to arthropod or vertebrate limbs; the regulatory system could have originally patterned any one of a number of outgrowths of the body wall in a primitive bilaterian for example.”

What do you think?

mjblyth - #65646

October 21st 2011

I don’t know enough biology to know what to think, but I agree that coincidence seems impossible. Sure, similar structures could develop, but regulated by the same systems by chance? One example (limbs) might just be believable, but you say there are others. The second explanation, of course, is quite satisfying if correct. I see it was proposed in 1997 ... any progress on it since then?

Is it possible that there is some structural connection between the developmental genes (or products) and their function, as is hypothesized in the case of codons and their corresponding amino acids (i.e. that it’s not a random code)? Could certain Hox genes  somehow have a connection with photopigments, for example?

Jon Garvey - #65644

October 21st 2011

“There’s also another more subtle reason: design in some form may be a necessary explanatory principle.”

That’s a very interesting observation, Steve. But I’m interested in how one defines “design” in such a case. Do you have in mind a concept where a naturalistically minded scientist would end up saying, “Well, design is clearly now necessary, but I can’t accept it because it’s giving god a foot in the door”? ID people would say that’s the position with origin of life studies, only the orthodox reply is usually denial rather than agnosticism “Design seems necessary, but we’ll find a fix somehow.”

Or does “design” in this context mean something more subtle in which there is not necessarily a designer, or where RM & NS is the pseudo-designer of pseudo-design (which is where, in loose terms, we seem to be at currently)? If so, what sort of mechanism have you in mind?

Surely in either case, for design to be “necessary principle” biological theory has to lack explanatory power without it, which would seem quite a radical departure from methodological naturalism.

mjblyth - #65645

October 21st 2011

Yes, I am unclear what is meant by “design” in this context, as something lacking in current theory but perhaps necessary. What is design if not the result of some intelligence? Could it refer to some platonic concept of ideals? Or? Convergence I understand, at least simple examples, but you mean more than that, right?

beaglelady - #65653

October 21st 2011

Excellent series, Steve. Thanks so much!

Re Simon Conway Morris, any thoughts on why God would be especially interested in saber teeth? 

beaglelady - #65703

October 24th 2011

I was hoping Steve would answer my question.  The last time the matter of saber teeth came up (must have been months ago, and by a different poster) and I had a question about the matter,  it, too, went unanswered.

btw, where has Pete Enns been? Hasn’t it been a while since he has posted anything?

sfmatheson - #65876

October 29th 2011

Hey all, I’m sorry I neglected these comments and questions.

myblyth #65646 asks: “The second explanation, of course, is quite satisfying if correct. I see it was proposed in 1997 ... any progress on it since then?”
You’ll find an excellent discussion of that question in the 2009 Nature paper I cite above. (The link takes you to a pdf copy of the article.) The authors discuss the development of beetle horns as a potentially informative example of the co-opting of the ancestral circuitry for a new purpose.
“Is it possible that there is some structural connection between the developmental genes (or products) and their function, as is hypothesized in the case of codons and their corresponding amino acids (i.e. that it’s not a random code)?”
It’s not currently possible to envision how this could be the case. The gene products are DNA-binding proteins that activate (or inhibit) gene expression. As far as we can tell, they do this without regard for the function of the activated genes. Might there have been an association in the deep past, as the system was being put together? I guess so, but it’s hard to picture.

sfmatheson - #65878

October 29th 2011

Both Jon and rjblyth are curious about what I meant by this statement: “Design in some form may be a necessary explanatory principle.”

There are a few possibilities here, all of which could be wrong. Here are two I have in mind.

1. Convergence might require further explanation, if it turns out that evolution appears to have a “directional signal.” (That last phrase is part of the subtitle of a 2008 volume, The Deep Structure of Biology, edited by Conway Morris.) That explanation might have to draw on some conception of “design space” (a phrase used repeatedly by Dan Dennett). Conway Morris and others talk of “general theories of organization.” It seems to me that “design” would have a place in such theorizing. What do you think?

2. Evolutionary trajectories at the molecular level, especially those that established the basic toolkit of life, could reveal patterns that require further explanation. (For example, it could turn out that the trajectories appear to be unreasonably efficient in finding solutions.) The reasoning is similar to that of convergence, but the phenomenon is completely different. Here, I think, the apt comparison is with cosmological fine-tuning, and the competing solutions are likely to be similar.

Re the first possibility, I think that Conway Morris is onto something, even though I don’t think that convergence has been strongly established as a concept in need of further explanation. As to the second, I don’t see strong evidence (or even mediocre evidence) for seemingly “guided” trajectories, and I doubt that any will be produced.

But those are a couple of the things I had in mind. Thoughts?

sfmatheson - #65880

October 29th 2011

beaglelady, could you rephrase the question? I don’t think I understand what you’re asking.

Jon Garvey - #65917

October 31st 2011

Hi Steve

1 My book budget hasn’t yet extended to looking closely at Conway-Morris’s explanations for convergence, so I’m underinformed. But as I understand it he postulates that things are set up so that the environment demands certain (limited) solutions from lifeforms. On the face of it I can’t see how that would ever go beyond, “Neat! So evolution’s even better grounded in law rather than contingency.” Could one ever explain the operating rules? So it would suggest fine-tuning, but unlike that in cosmology without the ability to say exactly what has been fine-tuned. Must read Morris, though.

2 “Unreasonable” must to some extent depend on worldview, and I suspect we might disagree on where the line is. But surely it needs to include hard statistics on specific changes taking place, the mechanisms involved and the resulting probabilities - all currently hard to come by. Taking the OOL example in my question, if laboratory work continues to fail to produce a candidate for a genuine self-replicating molecule, and a plausible mechanism for its original synthesis in nature, at some point something “unreasonable” ought to be deduced to have occurred. How long is a “reasonable” time to conclude that? Does the research need to have gone on as long as the original process, or do we know enough already?

beaglelady - #65924

October 31st 2011

beaglelady, could you rephrase the question? I don’t think I understand what you’re asking.

Are saber teeth a manifestation of intelligent design, something that God is especially interested in bringing about?  I don’t have the book, so I don’t understand the connection. At any rate, all critters with saber teeth are extinct.      

sfmatheson - #65927

October 31st 2011

Convergence is an observation about the patterns of evolution and need not imply a claim that particular aspects of the biological world are “manifestations of intelligent design.” I can’t speak for Conway Morris, but I think he would not suggest that every aspect of biology is optimized or that all evolutionary experiments will succeed. I don’t think the “failure” of saber teeth is a problem for his view of convergence. But I do think your question about failed experiments is an interesting one in the context of Conway Morris’ notion of a “map” of evolution.

If you want to explore his ideas and/or a nice collection of examples of convergent evolution, check out his brand-new website called “Map of Life” ( It’s a fun way to waste spend an hour or so.

beaglelady - #65929

October 31st 2011

Thanks for your reply!

Kirk Durston - #65984

November 3rd 2011

Interesting and informative article. I have a few comments …..

It does not logically follow that because one ‘can identify no clearly-defined principles of functional optimization’ that, therefore, the effect is not a product of intelligent design. A global functional optimum is unlikely if the limb/fin production system had to be flexible enough to function over a huge variety of environmental conditions, in a wide range of disparate machines/organisms, and survive countless error prone replications in all of the above.

My second comment is in response to the statement, “Design, to whatever extent it stands for functional optimization or even excellence ….”. I see this as a shift away from what I consider to be the primary question; does biological life require an intelligent origin? It does not logically follow that because a design may not appear to be optimized or excellent to us that, therefore, it did not require any intelligence to produce. For example, there are certain Mac devotees who strenuously argue that the Windows 7 OS is not even remotely close to an optimized system, forget about excellent, yet no one would argue that the Windows 7 OS did not require intelligence to produce. In general, and to answer the challenge in the article, as a former engineer I suspect that the more complex the system, and the wider range the demands and the more disparate the ecological niches, the more unlikely it will be that a global optimum will even exist for, say, a limb/fin development system; there may be a variety of methods and systems from which to choose. A highly flexible ‘fuzzy’ system may be the most robust but such systems are intentionally not optimized or ‘over fitted’.

I am also a wee bit skeptical of the assertion that unguided (by intelligence) common descent has an impressive amount of explanatory power. It certainly does within a species and maybe even within a genus. But for major taxonomic changes, the explanatory power begins to falter severely. Orphan genes, for example, form up to 1/3 of all genes in all genomes (Tautz & Domazet-Loso, (2011) ‘The evolutionary origin of orphan genes’, Nature Reviews Genetics, 12) and represent quantum jumps in functional information (as defined in the literature by Szostak, Hazen and Durston). Quantum increases in encoded functional information are not at all what one would predict under unguided (by intelligence) common descent, but they are precisely what one would predict if intelligence was involved in designing novel life forms, with or without a role for common descent.

Now let us consider the Hox gene complex. My hypothesis is that the ability to produce functional information is a unique attribute of intelligence. It can therefore be used as a ‘marker’ or ‘fingerprint’ of intelligence in design detection. It follows from this that if an effect requires or carries a statistically significant level of functional information then intelligence was required for its production. If one does not like this conclusion, one needs to falsify my hypothesis. I took a look at the Homeobox domain, downloading 12,029 sequences. Stripping out the redundant ones I was left with 5,964 unique sequences, a good sample size to calculate the amount of functional information required. The answer was 107 Functional Bits (Fits) of functional information. That represents a target size in sequence space of 10-32. The actual target size would be many orders of magnitude smaller than that, however, since I assumed site independence for the sake of simplicity. Bottom line: the fingerprints or marker of intelligence is all over the Homeobox domain, and that is just one small component of the Hox gene system. If one is going to assume unguided (by intelligence) common descent, then the Homeobox domain would have had to be discovered via an evolutionary search prior to the divergence of the arthropods and chordates … a ridiculously short time to locate such a minuscule target in sequence space (fixed by physics by the way) …. and that is just for the Homeobox domain, forget about the rest of the ‘deep homology’ hox gene complex. Yet an intelligent agent with sufficient background information on the laws of physics and coding could easily produce 107 Fits of information in minutes, seconds, or less. We do similar information-production feats every day.

Ultimately, the origin and diversity of life is a digital information problem working within the constraints of the laws of physics. A common designer, working under the common constraints of physics, encoding digital information in the genomes of life, producing quantum jumps in functional information represented by orphan genes, coupled with the high functional information ‘fingerprints’ of intelligence in novel life forms has substantially greater explanatory power than unguided (by intelligence) common descent.

sfmatheson - #65985

November 3rd 2011

Interesting comments.

Your first two paragraphs only make sense in the context of common ancestry, and that was of course my point. The last two sentences of the second paragraph make this most obvious: there would be no need for flexibility or fuzziness if organisms are designed de novo. You clearly agree, then, that design can’t supplant common descent.

I find your paragraph about orphan genes to be sadly misleading. For one thing, the subject of orphan genes is unrelated to your odd assertion that common ancestry “falters severely” during “major taxonomic changes” (whatever those are). Your preference for seeing “quantum jumps” in evolutionary history is yours to enjoy, but those who read the abstract you cite will discover that scientists do not share your view; instead, the authors are exploring the genesis of new genes and proteins from genomic precursors. (Readers new to this topic will also be interested in Bornberg-Bauer et al., “How do new proteins arise?” in Current Opinion in Structural Biology, 2010.) Readers of your comment should know that your “quantum jump” language is a rhetorical trick that obscures current scientific thought on the interesting question of formation of new genes.

Your comments on the homeobox exemplify one of the handful of common errors that is characteristic of the intelligent design movement. You provide quantitative estimates of “information” and “targets” that enable you to avoid consideration of the very assertion you need to defend: that evolution needed to hit precisely the “target” that you specify. This, indeed, was the main point I was making about design thought: that in order for your numbers to be relevant, you have to show that evolution had to discover the homeodomain – you have to show that it could not have been otherwise. Ditto for signaling systems and their receptors, for transcription factors and for kinases and for cytoskeletal proteins. That paragraph is a perfect illustration of one of the key weaknesses of your movement, and I note that it misses – or seeks to obscure – the main point of my final paragraphs.

I respect your preference for a designer’s-eye view of life, and I’m glad you agree that design can’t currently replace common ancestry as a sound explanation. You’ll have to do a lot better in the rest of your analysis; calculating the improbability of a specific evolutionary outcome is a trope that can’t fool everyone all the time.

mjblyth - #65987

November 3rd 2011

Kirk, by your hypothesis, when and how were all these genes inserted into their genomes by the designer? On your assumption that orphan genes designed, it would appear that they would have to be continuously designed and inserted from the beginning of life to the present, and presumably continuing now. What about the mechanism? Would the new genes just be created de novo, one second they are not present and the next second they’re inserted into the genome of enough organisms to yield a reproductively stable population? Or would they be mounted on mobile genetic elements  and use natural mechanisms to be incorporated? Or would an observer be in principle unable to distinguish this injection of information from natural processes?

Your calculations seem to assume that an entire gene would arise from scratch, having randomly explored the entire space of possible genes of that size, and that the only ones that would work are the ones we observe. I’m not a biologist, but I don’t think anyone is proposing this. You may want to check these two articles, which were referred to in a recent ID blog (sorry, I forget which!): “How much of protein sequence space has been explored by life on Earth?” ( and “Experimental Rugged Fitness Landscape in Protein Sequence Space” ( Of course there are arguments against both, but the articles give perhaps a better idea of what the probability challenges are than does your calculation.

Kirk Durston - #66006

November 4th 2011

sfmatheson wrote, “Your first two paragraphs only make sense in the context of common ancestry…

That would be incorrect. From a design/engineering perspective, if one is designing a component A for a wide variety of platforms that have to survive in a huge range of environments (pressures, aquatic and non-aquatic, temperatures and chemical) and must self replicate where errors can occur and accumulate, then it will be a bad idea if component A cannot be modified to suit a wide variety of applications, or has no flexibility, or is so fine tuned that the first error will result in a failure. A component that is highly flexible and modifiable is the way to go whether one goes for de novo design or common descent.

On the subject of orphan genes and quantum jumps: I gather from your comments that you read only the abstract but failed to read the paper. If you will read the paper, you will observe that the authors classify two types of orphan genes: those that have segments of sequence similarity with short segments in other non-coding areas, and those that do not have sequence similarity with anything else. This second type of orphan gene represents a true quantum jump in functional information. Denial of this is bad science that ignores the data. The authors’ invoke ‘De novo evolution’ where ‘In this scenario, randomly occurring sequence combinations would form cryptic functional sites … ” (p. 696)

So the question is, can ‘randomly occurring sequence combinations’ do the job? Science must be testable. Have you tested this ‘scenario’? Scenarios and creative story telling should not be confused with doing science. A scenario must be tested. We have data; the tests can be done. So I see orphan genes as empirical falsification for the theory of common descent as currently put forward. Furthermore, I see the functional information jumps required by the orphan genes as positive evidence for an intelligent input at that point. It is precisely what intelligent design predicts.

sfmatheson wrote, “in order for your numbers to be relevant, you have to show that evolution had to discover the homeodomain – you have to show that it could not have been otherwise.

The above statement and your comments that follow reflect a profound misunderstanding of the real world of intelligent design application. In reality, there may be any number of ways to write a computer program that will solve a complex problem, there may be endless variations on a jet engine and countless numbers of entertaining books written. Are we to therefore conclude that no intelligence was required for any of it? By your lights, no intelligence was required for the Mac OS Lion because there are potentially an endless number of other operating systems that could be written. I trust you see the flaw in your argument.

Perhaps a definition is in order that covers both ways the term ‘intelligent design’ is commonly used,

Intelligent design: an effect that requires intelligence to produce, the ability to produce effects requiring intelligence.

This definition applies to jet engines, genomes, software, the set of prime numbers from deep space, the Rosetta Stone and entertaining novels. You have, perhaps unintentionally, badly misrepresented intelligent design theory. Take a second look at the definition I have provided.

What is your scientific method to test for intelligent design? I don’t think you have one. Without a scientific method for design detection, you have no scientific grounds to reject the hypothesis that intelligence was required for the origin and diversity of life. Your ‘test’ of functional optimization certainly fails when applied to software, jet engines and entertaining novels, so what is your test? I would like to see something with a little rigour, maybe something with numbers at the end of it.

A test as to whether intelligence was required or not is simply this ….. was a statistically significant level of functional information required to produce the given solution? This is based on the testable, falsifiable hypothesis that, ‘the ability to produce statistically significant levels of functional information is unique to intelligence’. Now all we need is a method to measure functional information and we have a fully operational method to test for intelligent design, complete with equations and numbers. When we apply that method to biological proteins, they come up positive.

What is your method?

Kirk Durston - #66007

November 4th 2011

sfmatheson continued:

Finally, I see in your closing statement a classic illustration of
failing to deal with the real world data. Let us simplify the problem by
focusing on a single globular protein. Physics determines what
sequences produce stable, repeatable 3D structures, not biology. An
evolutionary search must find those. Have you any idea how tightly
constrained the biological proteins are? Pfam provides us with an
enormous amount of data to work with, a record of countless evolutionary
searches exploring the boundaries of fitness space for a given protein
family. To label actual results from real data ‘trope’ borders on
quackery. Real science works with real data to get real results. Once
the first protein is chosen, that vastly limits the next move, for that
protein will have to interact with something compatible. The further
along one gets, the fewer options are permitted. That is when common
descent, as commonly understood, starts to run into a wall. Not just any
old protein will do anymore; it has to fit with the system. Searches in
sequence space are forced to become orders of magnitude more specific.
Same goes for building a jet plane, writing software, or composing a
song. Before one starts, the choices are endless. Once one has started,
and the further along one goes in the chosen path, the more tightly
constrained the choices are. The end result is measurable in terms of
functional information, however, which will tell you how much
intelligence was required, not to start the process, but to produce the
end result. It is absolutely essential to grasp this.

Kirk Durston - #66008

November 4th 2011

mjblyth: In answer to your first question, I suppose we could look at ourselves for one possible approach. Imagine that you and I were designing and building an entire ecosystem for a remote planet. We could do it all at once or we could do it in stages, or as a smooth progression. It is quite likely that the variety of organic machines would demand that you and I come up with completely novel designs or modify existing designs and add to them, it would be a two-stage process. First is the mental/conceptual/planning stage that goes on in our minds. How that works I do not know. The second stage would be the physical implementation, physically getting involved to build the next organic platform. There is, however, an underlying principle here that I wish the reader to be crystal clear on. We can call it the grandmother principle.

Grandmother principle:
Grandmother may have no clue whatsoever how my laptop was mentally conceived, or how or when it was built, or even what it is, but it does not logically follow that no intelligence, therefore, was required to produce it.

Same goes for biological life. All we need to do is test for an intelligent input requirement as suggested above. Whether we know what kind of mental process was involved or how and when it was implemented are all interesting pursuits, but irrelevant to the test.

Your second paragraph mentions two papers. I personally discussed the first paper with its author when presenting some guest lectures at the U of Edinburgh and subsequently by email. There are serious problems with reducing the number of amino acids to only two or three that I can show from my own work. The author had no solution to those problems when I raised them with him. The second paper is interesting, but there are some significant questions. First, how much of the function of the g3p minor coat protein is contingent on the D2 domain? Is a relative fitness of 0.4 of the global peak sufficient for long term survival? If it is, then using published methods to measure functional information, virtually no information is required to produce it. My own ongoing work with protein families and domain families is showing that biological proteins seem to require a global optimum, not a local optimum. A rugged fitness landscape is actually detrimental to evolution as anyone with experience in genetic algorithms can testify. The authors rightly point out that, ‘On a rugged landscape, the adaptive walk can become trapped by local fitness optima. To find the global peak on the rugged landscape, the adaptive walk requires enormous sequence diversity.”

sfmatheson - #66010

November 4th 2011





Your responses are disconnected from the points that I have made in the original post and in my response to you. Little of what you have written is relevant to our discussion. I will explain in this comment, then address some of your specific claims in a subsequent comment. After that, I will let you have the last word, as I sense that you wish to use this forum to advance your ideas whether or not they pertain to the topics at hand.

You write extensively about whether “design” can be detected and about whether “flexibility” can be considered to be good design. I’m sure that both are true. As I have clearly stated repeatedly, in the original post and in the comments, I am arguing that design cannot supplant common descent without offering a competing  explanation. Your responses clearly indicate that design has not done this.

You write about what the intelligent design theory is. Whether or not you speak for the movement, your responses do not address my critique. Notably, you fail to understand or acknowledge that your detection of “design,” valid or not, fails to establish design as an alternative to common descent. You seem not to understand why it is an error, and a major one at that, to perform calculations based on the assumption that a particular evolutionary solution (e.g., a homeobox) was the only solution to a particular problem.

You write about “real results” and “real data,” as though there are published analyses that demonstrate the obvious truth of your hypotheses. While I await publication and vetting of such findings, I ask you to re-read the last few paragraphs of my original post, wherein I note that such work could indeed bolster design proposals in the context of common descent. In the meantime, I am unimpressed by your claims regarding protein structure and evolution, probably because I’ve read the recent work of experts in the field. My point is most certainly not that scientists know the origin of every gene, nor am I asserting that design claims have been conclusively ruled out vis-a-vis protein evolutionary trajectories. I am arguing that common descent is the context in which such ideas must be placed.

Sadly, you seem not to acknowledge that I am affirming design as a potentially useful concept in the analysis of evolutionary trajectories. I guess there’s nothing I can do about that, except to say that you will not make progress in your work as long as you persist in calculating “information”-based probabilities of single evolutionary outcomes. That is indeed a trope that will not fly among experts.

sfmatheson - #66011

November 4th 2011




Kirk, two responses to specific claims of yours, then you can wrap this up.

1. I was completely baffled by your claims regarding the Tautz & Domazet-Lošo article, especially your suggestion that I’ve not read it. (I’ve extensively reviewed some of their recent work at Panda’s Thumb, and read the paper you cited as soon as it came out.) I wrote that “the authors are exploring the genesis of new genes and proteins from genomic precursors.” That’s what the whole review article is about, including the section you pulled your tiny quote from. Here’s the paragraph from which you took the quote:

“In this scenario, randomly occurring sequence combinations would form cryptic functional sites (for example, transcription initiation regions, splice sites and polyadenylation sites) and would come under a regulatory control to produce a distinct processed RNA transcript (FIG. 3). This RNA could initially function as an antisense or structural RNA and would eventually acquire a functional ORF from which a completely new protein could evolve. The most stringent criterion for indicating the involvement of this mechanism requires that the corresponding genomic region of the gene is present in outgroup organisms, but as a noncoding stretch that is neither transcribed nor translated. Although this possibility for the emergence of new gene functions initially seemed the least likely, there are now a number of fully documented cases supporting de novo origination by this mechanism (BOX 2). In addition, several surveys identified many more candidates for possible de novo evolved genes in various species.”

With all due respect, I cannot understand why you would want to suggest that Tautz & Domazet-Lošo contradict what I wrote, nor do I comprehend the basis of your “quantum jump” view.

2. You wrote, “Have you any idea how tightly constrained the biological proteins are? Pfam provides us with an enormous amount of data to work with, a record of countless evolutionary searches exploring the boundaries of fitness space for a given protein family.”

In fact, “biological proteins” exhibit dramatic diversity in their level of “constraint,” and biologists studying protein evolution discuss many concepts in addition to constraint. As I’m sure you know, given your interest in the topic, these concepts include robustness, flexibility, dynamism, disorder, even instability (more precisely, marginal stability). Some enzymes are multifunctional; indeed, there are examples of proteins that switch between alternative structures. While I’m sure you’ve read the 2010 review article I mentioned in my first response to you, other readers have likely not seen it, so I will simply say that for me, there is a remarkable contrast between that article (with 71 references in its nicely annotated bibliography) and your stark assertion regarding “tightly constrained” proteins. I will not suggest that you have failed to read the article or the major studies that it cites, but I will say that I cannot understand why you make the claims that you do regarding protein evolution given the knowledge you surely possess. Specifically, I cannot understand why you would choose to emphasize “constraint” to the exclusion of all other pertinent knowledge about protein structure, function, and evolution.

I wish you the best in your continuing work on protein evolution and design. I hope you’ll consider re-reading my original post to discern my intent and my stance toward design. We might not disagree as much as it seems.

Kirk Durston - #66026

November 7th 2011

sfmatheson, I suggest that your perception that most of what I have written is irrelevant to the discussion is a symptom of what happens when two people are talking about the same thing, but from two very different levels of understanding. The result is that much of what one person says is not understood as important or even relevant by the other person.

I resist the assertion that common descent is the best explanation and design ‘has failed’. My problem is not with the evidence (offered in the ‘New limbs from old fins’ series) that supports common descent, but with the growing evidence that suggests that common descent is woefully inadequate, at best. The ‘New limbs from old fins’, therefore, can be misleading. A core aspect of the scientific method is falsification; we need to pay attention to mounting, severe problems in our theory. Common descent is not going to work without an enormous amount of controls and guidance precisely as it would if we were building/evolving/designing a wide selection of life forms in a lab ….. and the evidence of that enormous amount of guidance will be left behind in the form of functional information encoded in the genomes of life. What we are doing today, in the 21’st century, as we build artificial proteins and genes, is a classic example of intelligent design at work in the lab. As our knowledge of genetics, regulation and protein folding increases, the creative common descent story telling is increasingly sounding like quackery to the critical thinker. Either the 19th-20th century theory of common descent must be relegated to the dustbin of history, or it must be radically revised to include guidance by an intelligent agent on a massive scale ….. and the evidence for such design is there in the form of functional information and very impressive regulatory software that we are only beginning to reverse engineer. This is no longer ‘common descent’ as generally understood. I’m not even sure that the term ‘common descent’ will have any practical use under this more advanced approach.

I’m a detail person. Broad-brush explanations supported by selective evidence does not do it for me if increasing numbers of falsifying observations are being glossed over. Most recently, my research has been focusing on what the functional information in genes means in terms of sub-domain site interdependencies within the structure of proteins. There is an enormous amount of detail that can be resolved.

Much of what I read by scientists in the area of the origin and diversification of life, including ‘News limbs from Old’ above (with all due respect) suffers from a severe lack of critical analysis. I see an eagerness, indeed a complete confidence that this must be true, so no need to concern oneself with a critical focus on some of those pesky details; a creative scenario will do just fine instead.


Kirk Durston - #66027

November 7th 2011

Regarding my concern that ‘critical analysis’ when reading is not happening, let me point out two examples,

  1. the contention that I am assuming that a particular solution was the only one and,
  2. that Tautz’s and Domazet-Loso’s review of work in the area of orphan genes somehow satisfies the critical thinker as to how common descent produced orphan genes.

Regarding (1): I am mystified as
to how one could both have critically read my last post and concluded
that (1) is the case. I made it crystal clear that at the beginning of
any design project (or evolutionary project) there may be any number of
options. But as the project advances, the choices already made
considerably constrain the number of functional options still to be
chosen or ‘found’. A chronic mistake is assuming that as evolution
progresses, the future options are always endless. If one wants to build
a car and the first step is to commit to a 9/16” bolt, then one
automatically commits to ‘finding’ something with a female 9/16” thread.
Same goes for countless protein-protein interactions. The options are
first of all constrained by physics (most amino acid combinations will
not form stable, repeatable 3D structures). Next, the options are
constrained by function. Those two constraints narrow the options
down exponentially as the organism is ‘designed’ or ‘evolved’. The
physics constraints are a constant, but the functional constraints tighten exponentially as the project proceeds.

Regarding (2):

The fact that scientists are working on it does nothing to give me
confidence given what I know about physics, evolutionary algorithms, and
papers focusing on the physics of protein folding. Alchemists were
working on converting various substances to gold, but ultimately failed
and for good reason. A critical reader of that review would have noticed
that the key first step in an evolutionary scenario is ‘randomly
occurring sequences’. What I would expect a critical thinker to do is to
say, ‘Let us test that scenario ….. Physics determines the right
combinations to produce stable, repeatable globular structures, so how
hard a project is it to locate these special combinations in sequence
space that physics as a priori determined? If we do find
precursors to a ‘founder gene’ in a noncoding section, how did that
happen? Given what we know of physics and the rarity of stable,
repeatable combinations, how did we get some of the partial ‘answers’
against so impossible odds? ….. what is going on here?’ What are the
implications when we test this with genetic algorithms? There is an
upper limit to the number of options when it comes to the type of
protein folds. There are publications dealing with the taxonomy of
protein folds (observed and in theory) that if a believer in the power
of evolutionary searches were to actually think about, might result in a
lot of sleepless nights .... perhaps even a crisis of faith in the
adequacy of unguided evolutionary search engines to even get the minimal
genome off the ground.

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