Loops, New Challenge to Evolution

Loops in LeafAs a student at Christ’ College in Cambridge (1827-1831), Charles Darwin is reportedly given his first microscope by one of his insect collecting friends, John Maurice Herbert. Today, scientists use satellite nanoscopes to study intracellular molecular dynamics and signaling networks between cells.

While loop networks have long been used in architecture, their discovery in biology is credited to Uri Alon of the Weizmann Institute on Science. In 2002, Alon published a by entitled “Network motifs in the transcriptional regulation network of Escherichia coli” in the April edition of the journal Nature Genetics. These loop networks, however, present yet more challenges to the theory of evolution.

Alon discovered a large set of previously unknown gene regulation networks in bacteria. Since then, investigators have successfully expanded the search for the existence of looping networks in neurological and vascular tissues.

Complex loop network patterns are increasingly being recognized scattered throughout nature: in plant leaves, in the brain’s cerebral vasculature, arrays of fungi living underground, even within the convoluted shape of a foraging slime mold.

Loops in Eifel Tower IILooping patterns have long been used in architectural engineering. The metal bracings of the Eiffel Tower in Paris stand as a classic example of complex pattern of nested loops. Loops, like redundant computer networks or electrical grids, make processes and structures resistant to damage.

In a Quanta article “In Natural Networks, Strength in Loops,” science writer Emily Singer notes “for all the natural examples of loop design, surprisingly little is known about why the networks in leaves and the cortical blood vessels are organized in this way.”

In an interview, Marcelo Magnasco physicist at Rockefeller University explains the challenge: “We understand the physics of the connections between entities in full, disgusting detail; nevertheless, we do not understand the pattern as a whole. We don’t know why they look this way or why every tree is different.”

Investigators are now beginning to quantify the physics of loop networks to provide resistance to the damaging effects of fluid flow fluctuations in nature. The current focus of research has centered on tree leaves and human vascular systems.

“Plants are a spectacular system to work on as a physicist, because they are beautifully mathematical,” said Eleni Katifori, a physicist at the Max Planck Institute. “The hope is that if we understand the architecture of veins, we will get a better handle on photosynthetic efficiency in plants.”

Discovering a natural mechanism to account for an evolutionary development of these complicated loop networks is challenging a central unguided tenet of the evolution industry. According to the Evolution 101 website sponsored by the University of California, Berkeley (UCB), evolution proceeds from “chance changes”−not by design.

University of Chicago professor Darwin advocate, Jerry Coyne, weighs-in on his Why Evolution Is True website, “like all natural processes, [evolution] is purposeless and unguided.”  The unguided process of evolution by chance – not purpose – is a deeply rooted tenet of the evolution industry.

Unguided evolution by chance is not an “add on” tenet. Casey Luskin of Evolution News and Views explains: “the ‘unguided’ nature of Darwinian evolution is not a mere metaphysical ‘add on.’ Rather, it’s a core part of how the theory of Darwinian evolution has been defined by its leading proponents.”

The ubiquitous evidence for complex loop networks throughout nature emerges as a new challenge for any unguided process. In a recent study by Eleni Katifori and Magnasco published in PhoS One entitled “Quantifying loopy network architectures” discovered in trees “a hierarchically-nested architecture containing closed loops at many different levels” Like the design of the Eifel Tower, looping networks is not the result of some unguided chance process.     

Katifoni and Magnasco propose “a robust mathematical description of the network architecture” of loops “which are ubiquitous in both natural and man made structures”−the antithesis of an unguided chance process.

For biological evolution to be a “scientific fact,” evidence for the development of loop networks via a natural process is now essential. Loop network join the growing list of challenges facing the development of a new comprehensive theory of biological evolution.

As Eva Jablonka of the Cohn Institute and Marion J. Lamb of the University of London lamented in the watershed book entitled Evolution the Extended Synthesis :Challenges to the Modern Synthesis [neo-Darwinism] have been coming from many directions, most notably from developmental biology, microbiology, ecology, animal behavior, and cultural studies.”

The likelihood of a new theory emerging, though, is daunting. “No new theory,” Massimo Pigliucci of City University of New York (CUNY) noted in Evolution the Extended Synthesis, “has ever been declared itself from beneath a heap of facts.”

While evolution was once a theory in crisis, now evolution is in crisis without even a theory.

Biological evolution exists only as a philosophical fact, not a scientific fact.

27 Responses to “Loops, New Challenge to Evolution”

  • Joe Dickinson:

    This is perhaps the weakest in a long series of feeble attacks on the central theory of all modern biology. The whole point of Darwinian natural selection is that it produces the “appearance of design” without the need for a designer. This particular example poses no challenge whatsoever to that paradigm. Give it up!!

  • MaryAnn:

    Joe, scientists question. It is the nature of science to ask “How”?, not to give up.

  • The principle purpose of science is to discover the laws of nature by testing the evidence for and against proposed theories for the law. To “give it up” is the very antithesis of science. Science unveils destroys myths – like Darwinism. Design requires a designer, even Darwin acknowledged that.

    The final stages of neo-Darwinism, from a scientific perspective, entered the picture about 2 decades ago following the demise of true Darwinism at the beginning of the last century.

    Consider reading some these latest books that spell-out the death of the central dogma of neo-Darwinism: The End of Darwinism, Signature in the Cell, Evolution a View from the 21st Century, Why a Fly is not a Horse, Nature’s Destiny, Altenberg-16, Mind and Cosmos, Science and Human Origins, Darwin’s Doubt, and Evolution, The Extended Synthesis – to name just a few.

    As Massimo Pigliucci and Gerd Műller – co-editors of Evolution, The Extended Synthesis – explain, “All of these molecular processes clearly demolish the alleged central dogma [neo-Darwinism].” Darwinism and neo-Darwinism are dead as scientific theories – and only now lives within the realms of science fiction.

    Before giving up, consider examining the scientific evidence.

  • Joe Dickinson:

    Or perhaps you should read something by an actual evolutionary biologist. “The Blind Watchmaker” is still the best exposition of the mechanism and logic and “The Greatest Show on Earth” and “Why Evolution is True” summarize the overwhelming evidence. “Darwinism is dead” is nothing more than wishful thinking.

  • Actually, Dawkins’ “The Greatest Show on Earth” and Coyne’s “Why Evolution is True” are in my library which I have read cover to cover.

    Just from these two books, in your opinion, what is the most impressive physical evidence presented to support the evolution of one kind, like a bacteria, into another kind, like a trilobite?

  • Joe Dickinson:

    “Kind” is a poorly defined, unscientific and remarkably flexible concept. As far as I can tell it basically means “a group within which we can’t even hope to deny evolution”. So, for example, if we are talking about Archaeopterix, kinds seem to be birds and reptiles (classes). So evolution from hummingbirds to ostriches, lizards to crocodiles would be fine. If we apply that definition to mammals, shrews to humans and pigs to whales should be accepted. But no, for mammals, kind (sometimes) seems to equal order (e.g., dogs vs. cats, bats vs primates). Fine, that still allows evolution from monkeys to humans. But, as we approach humans, “kind” seems to contract to genus or even species. What you are “preaching” (a term chosen with some thought) is ideology, not science.

  • Just wondering – in your opinion, from these two book that you wanted read to prove that evolution is true, what was the most impressive physical evidence for the change from one kind to another kind. Use whatever kind or species you think best represents an example of biological evolution.

  • Joe Dickinson:

    Give a clear, consistent and firm (i.e., non-slippery) definition of “kind” and I will try to respond. Preferably, pick one (and only one) of the categories understood and accepted by actual scientists (species, genus, family, order, etc.) ( i.e., you can’t use class = kind when talking about birds, order = kind when talking about non-primate mammals and species = kind when talking about primates).

  • I agree with the argument being discussed in this posting. Without getting lost in technical details, Richard presents the dilemma that complex intertwined biological systems mean for evolution. How these interlocking systems could spontaneously arise incrementally through random mutations is insurmountable. This screams of design.

  • Just select any of the “kinds” you want as used by either Dawkins in “The Greatest Show on Earth” or Coyne’s “Why Evolution is True.”

  • Joe Dickinson:

    So, I will take that as an admission that you can’t actually define “kind”. I don’t have them to hand, but I’m pretty sure neither Dawkins nor Coyne ever used “kind” in anything like the sense you imply (but perhaps, to ridicule this meaningless creationist concept). If I’m wrong, cite “chapter and verse” (so to speak). Otherwise, admit that what you do is about faith, not science.

  • Please use something else as an example of evolution from Dawkins’ or Coyne’s book – other than “kind” then.

  • Joe Dickinson:

    Game, set , match.

  • Robert Leonhard, Ph. D.:

    One of the most valuable aspects of this website for me is the response of Darwinists. I like to read their perspective and find myself hoping that they will offer a respectful insight that we can consider. I note, however, that almost invariably they resort to ad hominem and personal attacks instead of arguing dispassionately. It is odd to me that anyone who claims to be a scientist would automatically rule out a designer–as if that idea is somehow unscientific. True science should not rule out anything, and should never be afraid of where the evidence might lead. And a cursory reading of the history of science would point to a long, unbroken chain of scientific theories being later disproven. Indeed, the very basis of science is the assumption that we MIGHT be wrong.

  • Joe Dickinson:

    OK, you can’t define kind, so, by answering, I risk the response “well, that’s not real evolution because it’s still the same kind”. As I said before, “kind” seems to be pretty flexible as used by creationists and the ID establishment, basically meaning “a group within which I can’t possible deny the evidence for evolution”. Anyway, here goes. In science, the most powerful evidence comes when completely independent lines of inquiry reach the same conclusion. In the case of evolution, at least three kinds of evidence are relevant: comparative anatomy/embryology, fossils, and DNA sequence comparisons. There is, as far as I know, no case in which these diverse approaches contradict one another. For creationists/IDiots, that can only be viewed as a remarkable coincidence. For evolutionists, it is exactly what we expect. A specific case: comparative anatomists suggested a few decades ago (based, I believe, on some details of cranial anatomy), that whales are closely related to ungulates (hoofed mammals). Creationists ridiculed this suggestion. Since then, A wonderful series of fossil intermediates has been found linking terrestrial mammals through amphibious types (rather like sea lions) to fully aquatic forms that still had functional hind limbs (with little hoofs on the toes!) to modern whales (with no functional hind limbs but still a pelvis and hind limb rudiments buried deep within the body. What sort of intelligent designer would do that?). Then the DNA evidence came in. Not only are whales close to ungulates, they are nested within ungulates (i.e., whales are closer to some ungulates, such as hippos, than those ungulates are to others). Can you give a rational non-evolutionary explanation for those facts? I didn’t think so. And this sort of concordance is repeated time after time after time. An evolutionist challenged with “what is the evidence for evolution” often is at a loss since the real answer is “everything I know about biology”. Do you have the courage to post this comment?

  • Joe Dickinson:

    To Robert Leonhard: Excuse me for being passionate about truth and the real scientific method. Creationism and ID start with a conviction about what is true and seek “:evidence” to support that pre-conviction. Here is my challenge to you: describe an observation that would convince you that ID is false. If you can’t imagine an experimental refutation, it isn’t science. Note: there are many possible observations that would refute evolution (e.g., the independent lines of evidence described above give contradictory answers). Evolution has been exposed to many possible falsifications but survives just fine. Meanwhile, ID has made not one useful prediction. I will be respectful when/if you earn some respect.

  • Good discussion. One of your the opening comments said that I should get educated about evolution by reading either one of Dawkins or Coyne’s books. However, I stated I have copies of both books in my library which have been read cover to cover. Then, I asked if you could provide from either one of these books what specific evidence you found to be the most convincing in favor of evolution. Correct me if I am wrong, but you have yet explained what was the most evidence you found in those books that was most impressive to you. It is becoming apparent that you have not read either of these books.

    Since your comments are generalities, not specific scientific evidence, let’s get back to the original question again: “in your opinion, from these two book that you wanted read to prove that evolution is true, what was the most impressive physical evidence for the change from one kind (or species) to another kind (species). Use whatever kind or species you think best represents an example of biological evolution.”

    Just as an FYI – creationists are of the opinion that life is supernatural – not dependent on some natural mechanism. Evolutionists, since they believe that life is the result of natural processes and laws, are at the mercy of finding l evidence for “slight successive” physical changes from species to species. So far, you have not shown the required “slight successive” physical changes from species to species – or from kind to kind – or however you would like to phrase different life forms.

    Looking forward to what you think is Dawkins’ or Coyne’s best evidence for evolution.

  • Let’s flip your question around, what falsifiable evidence exists to support evolution?

    Your comment “evolution has been exposed to many possible falsifications but survive just fine” is interesting. If evolution is true, just what theory of evolution are you talking about. Is it Darwinism, neo-Darwinism, modern synthesis theory, symbiotic cell theory, evo-devo, epigenetics, niche inheritance, self-assembly theory, behavioral evolution, sympatric speciation, or some of the other thousands of theories of evolution.

    In the words of Jacques Monod, “a curious aspect if the theory of evolution is that everyone thinks he understands it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually, as it stands, even as it stood when Darwin expressed it, and even as we now may be able to understand it in biology.”

    Unfortunately, “a fully unified view of evolutionary processes may be out of reach” is one of the concluding remarks in Evolution, the Extended Synthesis edited by Massimo Pigliucci and Gerd B Műller.

    Looking forward to what you think is Dawkins’ or Coyne’s best evidence for evolution.

    Biological evolution exists – but only as a philosophy – not as a science.

  • Joe Dickinson:

    Did you not read my comment about evolution of whales? I think both Dawkins and Coyne discuss those examples. First let’s distinguish between the historical fact of evolution (no more controversial than gravity or atomic “theory”) and the “theory” that accounts for that fact. The things you list as alternative theories of evolution are mostly just different aspects of one theory . No controversy, no need to make a choice. All are subsumed within Darwinism. FYI:”supernatural” basically means “not subject to scientific inquiry”. What you basically admit is that “evolutionists are at the mercy of finding evidence”. So creationist are exempt from considering evidence? That is not science!! So why do you insist on claiming what you do is sciences?

  • What book and pages are you referring to?

  • Joe Dickinson:

    As I mentioned, I don’t have either book to hand, but my comments stand on their own. Have read them? Understood them? If you must, go to Coyne’s web site, “Why Evolution is True” and use his search function to look for “whales” It’s all there. Try also chapter 6 of Dawkins book. But, come on! Why are page numbers more important than facts and a clear argument?

  • Actually, facts – scientific facts – are far more important than any argument. So far, however, you have only have arguments – no facts. It is very interesting you are arguing in favor of books you have never even read. That practice will not give you many credibility points. I often check out Coyne’s site. The articles and comments are about as worthless as your rhetoric – I have even seen your posts on the site. Telling someone to go read something for yourself, however, is the type of scientific argument expected of junior high students.

  • Joe Dickinson:

    I have read both books, just don’t own them – you have heard of libraries I presume. Fossils of intermediates leading to whales are facts. DNA sequences relating whales to ungulates are facts. And on and on.

  • OK, then could you identify exactly what the fossil intermediates leading from the whale to the ungulates and identify exactly what DNA sequences have changed from the whale to the ungulates?

  • Interesting discussion. What I note is that the pro-evolution stance is this: “If I can make a story that shows that some evidence doesn’t absolutely disprove evolution, that proves that evolution happened.” There is no attempt to show by real observation that evolution actually happened (not that it might have happened). There is no attempt to show by real observation that Creation did not actually happen. And yet, this is the real question. Which one happened. God says that He created everything.

  • “You have not absolutely proven that evolution could not have happened, and the majority of scientists believe that evolution did happen, therefore evolution must have happened” is not sound reasoning.

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