Monday, June 15, 2015

The meaning of "irreducible complexity"

Michael Behe first proposed the idea of "irreducible complexity" in Darwin's Black Box back in 1996. He defines it as ...
By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. Since natural selection can only choose systems that are already working, then if a biological system cannot be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on.
A recent paper published in Cellular and Molecular Life Sciences has attracted the attention of the Intelligent Design Creationists because it mentions irreducible complexity. According to Denyse O'Leary (? News) the paper "uses “irreducible complexity” in same sense as ID theorist Behe?" [see Refereed paper in Cellular and Molecular Life Sciences uses “irreducible complexity” in same sense as ID theorist Behe?].

That's interesting. Let's look at the paper to see what it says. The reference is Muskhelishvili, G. and Travers, A. (2015) and the relevant passage is on page 4556.
Thus, the holistic approach assumes self-referentiality (completeness of the contained information and full consistency of the different codes) as an irreducible organisational complexity of the genetic regulation system of any cell. Put another way, this implies that the structural dynamics of the chromosome must be fully convertible into its genetic expression and vice versa. Since the DNA is an essential carrier of genetic information, the fundamental question is how this self-referential organisation is encoded in the sequence of the DNA polymer.
What they are saying is that proper gene regulation requires both transcription factors AND a particular organization of the chromosome that facilitates transcription. It also requires input from metabolic pathways. If any one of these three things are missing then the cell cannot regulate gene expression in the same manner as cells where all three are present.

The authors then go on to discuss how this system could have evolved. Look at Figure 3 of their paper (below) where they clearly show the relationships between transcription, supercoiling, and small regulatory molecules. The paper describes their belief that this "irreducible organisational complexity" arose by evolution from these three existing features.


So, these authors are using "irreducible complexity" to describe a system that's clearly possible according to their understanding of evolution. Uncommon Descent states that this is exactly the same sense in which the term is used by Michael Behe. In fact, it quotes a physicist named David Snoke who says,
Three comments: 1) the authors are “serious” scientists, not fringe people. 2) They are using “irreducible complexity” in the same sense as Behe. This is not a case of accidental use of the same phrase to mean something different. Their term “holistic” is another way of saying the same thing, that the system requires all of its parts to work. 3) This “holistic” approach is one that is becoming common in systems biology. I have a paper coming out on that, in the works.
We've been telling Intelligent Design Creationists for years that irreducibly complex systems can easily arise by naturalistic processes (i.e. evolution). I'm really glad that they have finally seen the light.

That should be the end of any more posts saying that irreducibly complex systems can't evolve.

(Not holding my breath.)


Muskhelishvili, G. and Travers, A. (2015) Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information. Cell. Molec. Life Sci. 70:4555-4567. [Abstract]

28 comments :

  1. Post that on Uncommon Descent, I dare you!

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    1. Don't worry. No doubt one of their brightest minds (vjtorley? kairofocus? Barry Arrington? Denyse O'Leary?) is working on a response as we speak. I'm sure Larry is quaking in his shoes at the devastating take down that is to come.

      Or not.

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  2. creationist cherry picking at its finest

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  3. The case for IC is unaffected by this paper. Even if these researchers, huess, at how it could evolve it doesn't affect IC.
    IC also is not just denying how it could evolve but how something is still so complex after all attempts to reduce THAT is means its beyond chance to come to that complex level.
    IC has two points really.
    Anyways having complexity evolve is still guessing. No one saw it.
    its easy to say a airplane or watch can create itself by using raw materials.
    Actually its not easy.
    One can't easily dismiss complex creations by speculations on their origin by chance.
    it needs a more complex answer.

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    1. Other than strained analogies and just-so stories, what is the actual evidence for ID in biological entities?

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    2. Their complexity is the evidence for a thinking being behind it!
      Chance is unreasonable much less demonstrable.

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  4. Irreducible is a DOA concept. Unevolvable would be a coherent concept. It might even be useful in analyzing a suspected GMO product.

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  5. This comment has been removed by the author.

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    1. Or simply a DUD (Dead Upon Departure)

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    2. There's this 2015 paper in PNAS where they sequenced whale DNA and found genes coding for two critical proteins in the anti-viral response missing in tooth whales, but these genes and proteins were present in non-tooth whales. The paper shows that even with 2 key genes and proteins missing, tooth whales still have a functional immune system. According to the definition of IC, the immune system couldn't have evolved without these 2 genes, thus tooth whales can't exist.

      The results are in line with what you would expect if the genes were passed along from a common ancestor of tooth whales, but after baleen and the tooth whale line split.

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  6. So, these authors are using "irreducible complexity" to describe a system that's clearly possible according to their understanding of evolution.

    The fact they don't make the connection shows how unfamiliar they are with thinking through the implications of what they've read and are purporting to analyze. It's of a piece with their allergy to any mention of Lenski when his experiments show how very difficult it is for evolution to traverse certain pathways far better than anything Behe's ever done.

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  7. The amazing organisation and design of DNA, genomes, histones, nucleosomes and chromosomes

    DNA, as a very stable nano-molecule. It is an formidable, ideal massive storage device for long-term data archive. 22 The organisation of this higher order structure of chromosomes and respective substructures is awe inspiring when looking closer at its features and functionality. DNA nanotechnology tries to mimic its capabilities since this type of storage system is more compact than current magnetic tape or hard drive storage systems due to the data density of the DNA. For example, DNA stores the information to make over 100.000 different types of proteins in the human body, each with a unique function. We think that we have done very well with human technology, packing information very densely on to computer hard drives, chips and CD-ROM disks. However, these all store information on the surface, whereas DNA stores it in three dimensions. It is by far the densest information storage mechanism known in the universe.

    Let's look at the amount of information that could be contained in a pinhead volume of DNA. If all this information were written into paperback books, it would make a pile of such books 500 times higher than from here to the moon! The design of such an incredible system of information storage indicates a vastly intelligent Designer. A paper , published in Nature, reports that "existing technologies for copying DNA are highly efficient," this makes DNA an "excellent medium for the creation of copies of any archive for transportation, sharing or security." The authors conclude that "DNA-based storage has potential as a practical solution to the digital archiving problem and may become a cost-effective solution for rarely accessed archives." 1

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    1. DNA, as a very stable nano-molecule. It is an formidable, ideal massive storage device for long-term data archive.

      "Ideal"? You know there are such things as mutations, right? Various forms of RAID architecture work better. So either DNA information storage wasn't designed, or the designer/creator was less competent than today's computer scientists, take your pick.

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  8. In Alberts book molecular biology of the Cell, we read : The structure and chemical properties of DNA make it ideally suited as the raw material of genes. The packing has to be done in an orderly fashion so that the chromosomes can be replicated and apportioned correctly between the two daughter cells at each cell division. We also confront the serious challenge of DNA packaging. Each human cell contains approximately 2 meters of DNA if stretched end-to-end; yet the nucleus of a human cell, which contains the DNA, is only about 6 μm in diameter. This is geometrically equivalent to packing 40 km (24 miles) of extremely fine thread into a tennis ball! The complex task of packaging DNA is accomplished by specialized proteins that bind to and fold the DNA, generating a series of coils and loops that provide increasingly higher levels of organization, preventing the DNA from becoming an unmanageable tangle. Amazingly, although the DNA is very tightly folded, it is compacted in a way that allows it to easily become available to the many enzymes in the cell that replicate it, repair it, and use its genes to produce proteins.

    Packing ratio - the length of DNA divided by the length into which it is packaged

    For example, the shortest human chromosome contains 4.6 x 107 bp of DNA (about 10 times the genome size of E. coli). This is equivalent to 14,000 µm of extended DNA. In its most condensed state during mitosis, the chromosome is about 2 µm long. This gives a packing ratio of 7000 (14,000/2).

    To achieve the overall packing ratio, DNA is not packaged directly into final structure of chromatin. Instead, it contains several hierarchies of organization. The first level of packing is achieved by the winding of DNA around a protein core to produce a "bead-like" structure called a nucleosome. This gives a packing ratio of about 6. This structure is invariant in both the euchromatin and heterochromatin of all chromosomes. The second level of packing is the coiling of beads in a helical structure called the 30 nm fiber that is found in both interphase chromatin and mitotic chromosomes. This structure increases the packing ratio to about 40. The final packaging occurs when the fiber is organized in loops, scaffolds and domains that give a final packing ratio of about 1000 in interphase chromosomes and about 10,000 in mitotic chromosomes.

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  9. In Wikipedia we read in this regard : DNA has a striking property to pack itself in the appropriate solution conditions with the help of ions and other molecules. Usually, DNA condensation is defined as "the collapse of extended DNA chains into compact, orderly particles containing only one or a few molecules" 4

    Furthermore: Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA). For example, each human cell has about 1.8 meters of DNA, (~6 ft) but wound on the histones it has about 90 micrometers (0.09 mm) of chromatin, which, when duplicated and condensed during mitosis, result in about 120 micrometers of chromosomes

    This is a amazing example of extraordinary design, unparalleled by human intelligence. Question: Is it not unlikely that natural processes could achieve this feat to condense DNA into such a enormously tiny , highly regulated and functional structure ? Why at all should it happen ?

    Dr. Stephen C. Meyer in his 1996 essay The Origin of Life and the Death of Materialism, wrote that
    "the information storage density of DNA, thanks in part to nucleosome spooling, is several trillion times that of our most advanced computer chips

    How could undirected natural processes have produced the most advanced storage system known in the universe ? Evolution is not not a explanation, since its depends on this very own storage system in order for natural selection to occur.

    Eukaryotic chromosomes consist of a DNA-protein complex that is organized in a compact manner which permits the large amount of DNA to be stored in the nucleus of the cell. The subunit designation of the chromosome is chromatin. The fundamental unit of chromatin is the nucleosome.

    Everything in the cell is organized and in its expected place and function. Nothing in the cell is left to chance. The nucleus is no exception. In fact, in some ways, the nucleus is more organized and complex than the rest of the cell. One aspect of the complexity and organization of the nucleus is the chromatin. 3

    Furthermore, in following paper, Integration of syntactic and semantic properties of the DNA code reveals chromosomes as thermodynamic machines converting energy into information, we find a true mind blower, showing the irreducible organizational complexity (author’s description) of DNA analog and digital information, that genes are not arbitrarily positioned on the chromosome etc. 5

    The paper argues that cellular mechanisms involved in processing genetic information make up an irreducibly complex system. The system requires genetic information, genetic machinery keyed to read that genetic information, as well as specific chromosomal organization. All of these components are necessary for what the paper calls "the organisational complexity of the genetic regulation system."

    To be precise, the paper uses the term "irreducible organization" but it amounts to the same thing as biochemist Michael Behe's "irreducible complexity," and points implicitly to the same challenge to Darwinian accounts of origins.

    1) the authors are “serious” scientists, not fringe people
    2) They are using “irreducible complexity” in the same sense as Behe. This is not a case of accidental use of the same phrase to mean something different. Their term “holistic” is another way of saying the same thing, that the system requires all of its parts to work.
    3) This “holistic” approach is one that is becoming common in systems biology.

    1) http://www.nature.com/nature/journal/v494/n7435/full/nature11875.html
    2) http://www.ndsu.edu/pubweb/~mcclean/plsc431/eukarychrom/eukaryo3.htm
    3) http://creationrevolution.com/chromatin-%E2%80%93-simple-cell-part-18/
    4) https://en.wikipedia.org/wiki/DNA_condensation
    5) http://www.evolutionnews.org/2013/10/paper_irreducib077761.html

    more: http://elshamah.heavenforum.org/t2017-the-amazing-organisation-and-design-of-dna-genomes-histones-nucleosomes-chromosomes#3392

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    1. "Leila" asks:

      This is a amazing example of extraordinary design, unparalleled by human intelligence.

      So the genome is totally unlike anything ever made by intelligent designers. Therefore it is exactly like a thing made by an intelligent designer.

      This is IDiot logic, as we have pointed out over and over and over.

      Question: Is it not unlikely that natural processes could achieve this feat to condense DNA

      Yes, it is not unlikely that natural processes could condense DNA. DNA is charged. Histones have the opposite eelectrical charge. Do you think it likely they should stay apart? You think it is likely for opposite charges to repel?

      Question: is it not unlikely that DNA condensation was created supernaturally by an invisible, benevolent and omnipotent man, who did this incredible DNA design 3 billion years ago, and then stood by and let baby animals and humans suffer for hundreds of millions of years?

      Who spent 1,000 years supernaturally assisting the Jews to genocide their neighbors, while repeatedly instructing them that 1. God is jealous and mean, 2. God is one and 3. must never be worshipped in material form... then after 1,000 years of that, takes the material form of a sex-hating rabbi who says 1. God is love and love is not jealous, 2. God is three persons, and one of them is a pigeon who took the form of a ghost to forcibly impregnate my teenage mom, 3. now worship me in my material form, or else I'll set you on fire forever, but in an invisible place where there's no evidence I burnt ya?

      How likely is that?

      into such a enormously tiny , highly regulated and functional structure ? Why at all should it happen ?

      DNA is charged. Histones opposite charge. Why do you think they should repel?

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    2. Now two more questions for "Leila" (certainly a dude): do you think *random sequences of DNA* will also be condensed by histones into chromatin?

      Every human baby has ~ 100 novel mutations its parents didn't have, and twice that relative to its grandparents, etc. Do those random mutations also get condensed by histones into chromatin?

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    3. Now we get to the IDiot authority quote, which is mandatory in IDiot comments.

      (A digression. What is it with you IDiots and your MAQs (mandatory authoriity quotes)? Why do you have to quote some DI con artist every single time? Did you IDiots have a meeting and vote that every one of you must copy and paste an authority quote on every occassion? You're like $%&#ing scientologists quoting L. Ron Hubbard. Can any of you make your own scientific argument from evidence alone, not from authority?

      I think IDiots believe a MAQ is mandatory because 1. They know Discovery Institute con artists aren't respected as scientific authorities and, if they can get us to discuss those lying fascist shits as if they are our equals, it creates the illusion that there's a controversy between trustworthy science authorities; and 2. ID proponents are afraid to form their own scientific argument in their own words because they know that they don't know the meaning of the science jargon words, and they know we'll mock them when they get it wrong, so it's safer for them to copy and paste. ... But I digress.)

      Back to today's MAQ. Since the topic is genomics, our IDiot naturally chose as her authority a Ph.D. in philosophy. Namely one Stephen Meyer, who has repeatedly confused nucleotides with amino acids, and viruses with bacteria. So he's your go-to man for molecular biology.

      Dr. Stephen C. Meyer in his 1996 essay

      (Typical creationist, calls a creationist philosopher "Dr." but doesn't call evolutionists "Dr." Again I digress.)

      Dr. Stephen C. Meyer in his 1996 essay The Origin of Life and the Death of Materialism,

      Stop right there. ID proponent Stephen Meyer announced the "Death of Matetialism" 20 years ago, that's twenty #$%&king years ago, and in the intervening two decades the percentage of atheists in the USA doubled, and that's not a red flag you're dealing with an IDiot?

      wrote that
      "the information storage density of DNA, thanks in part to nucleosome spooling, is several trillion times that of our most advanced computer chips


      Ah. Again we are told DNA is unlike anything made by any intelligent designers, therefore it is just like a thing made by an intellifent designer.

      Note that in the above, Meyer is measuring "information" under the assumption that the amount of "information" is directly proportional to the number of DNA base pairs (presumably 2 bits per bp), which means that any natural process that increases the length of DNA sequences increases the "information", and since natural processes like gene duplication occur naturally during evolution and increase the length of DNA sequences, therefore evolution increases "information" by the measure Meyer uses. Therefore, when we see information in DNA, we should assume by default that the infotmation is the product of natural processes unless evidence indicates otherwise.

      How could undirected natural processes have produced the most advanced storage system known in the universe ? Evolution is not not a explanation, since its depends on this very own storage system in order for natural selection to occur.

      Notice Meyer pulled a bait and switch. He says let's think about the most advanced forms of DNA storage (the bait). Then he says evolution can't do that because evolution requires DNA (the switch). True, but irrelevant to Meyer's point because 1. Evolution does not require the most advanced forms of chtomatin storage, it only requires self-replication, and 2. Other things can do self-replication and evolution besides DNA organized into chromatin, e.g. bacterial DNA and self-replicating RNA.

      To this I will add: "intelligent design" is no explanation at all, because intelligent designers need to store the information for their model blueprints somewhere. Meyer has no evidence of the existence of supernatural mechanisms for storing information.

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    4. When you have DIRECT and PRECISE answers to my questions, and stop name calling the counterpart, we talk.

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  10. Laurence, so how about you start and explain in detail HOW evolution produced these things, and specially in what order ??

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    1. Either that or "God-did-it"? Do you understand how irrational it is to think that open questions mean that there's gods?

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    2. How many of you agree that Leila = Quest?

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    3. and specially in what order

      Simple answer: Google "evolution" along with "nested hierarchies."

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  11. Why not offer an evidence based alternative. In detail.

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  12. Why not offer an evidence based alternative. In detail.

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  13. I seriously think the problem is from over-complicating the argument. Only thing it needs to be true is that the system from which our design was created somehow qualifies as "intelligent" in which case intelligence was required.

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    1. Sure. And if it "somehow qualifies" as "pink strawberry flavoured candy floss" then pink strawberry flavoured candy floss was required. Your point being....?

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  14. Is the living cell able to evolve by Darwinian mechanism? Can you provide the evidence your science is based on? I'm sure you are not making up if you do.....

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