Intelligent Design

Isolated complex functional islands in the ocean of sequences: a model from English language, again.

Spread the love

 

 

 

A few days ago, Denyse published the following, very interesting, OP:

Laszlo Bencze offers an analogy to current claims about evolution: Correcting an F grade paper

Considering that an example is often better than many long discussions, I have decided to use part of the analogy presented there by philopsopher and photographer Laszlo Bencze to show some important aspects of the concept of isolated islands of complex functional information, recently discussed at this OP of mine:

Defending Intelligent Design theory: Why targets are real targets, probabilities real probabilities, and the Texas Sharp Shooter fallacy does not apply at all.

and in the following discussion.

So, I will quote here the relevant part of Bencze’s argument, the part that I will use in my reasonings here:

You stand in for evolution and your task is to convert a poorly written “F” paper to an essay that can be published in Harper’s Magazine. This is reasonably analogous to fish evolving into an amphibians or a dinosaurs into a birds.

However, your conversion of the inept essay must proceed one word at a time and each word substitution must instantly improve the essay. No storing up words for future use is allowed.

After changing a few obvious one-word mistakes, you will run into a brick wall. It doesn’t matter how clever you are or how many dictionaries and writers’ guides you have at your disposal. Only by deleting entire paragraphs and adding complete sentences would you have any chance of getting to a better essay. But that would be equivalent to a small dinosaur sprouting functional wings or a fish being able to breathe air in a single mutation. Changing one word at a time and expecting that to result in better writing is hopeless.

Well, I will reshape a little this analogy, so that it fits my purposes. The aim is to show realistically the meaning of some concepts and ideas related to funtional information. I have already done something similar in an old OP, that I will refer to when necessary:

An attempt at computing dFSCI for English language

Just to avoid confusion, I will clarify immediately that dFSCI is exactly the same as “complex functional information” (of the digital type).

Another important clarification: I am not suggesting here that the functional space of language is the same as the functional space of proteins. They are, of course, different. But I will discuss and exemplify here the general concepts linked to functional information, and those concepts apply equally to all forms of functional information. Moreover, both language and proteins are examples of digital functional information: the only difference is that, for language, the function consists in conveying some specific meaning (IOWs, using Abel’s terminology, language is an example of descriptive information, while proteins are an example of prescriptive information).  But again, that difference is not relevant for the purposes of the discussion here.

So, my model goes this way. We start form an essay, written in English language. Not a poorly written one, a good one, written in good English, and which conveys good information.

As an example, I will quote here a few paragraphs from the Wikipedia page about “History of combinatorics”:  (OK, it’s a little self-referential, may be! 🙂 )

The earliest recorded use of combinatorial techniques comes from problem 79 of the Rhind papyrus, which dates to the 16th century BCE. The problem concerns a certain geometric series, and has similarities to Fibonacci’s problem of counting the number of compositions of 1s and 2s that sum to a given total.

In Greece, Plutarch wrote that Xenocrates of Chalcedon (396–314 BC) discovered the number of different syllables possible in the Greek language. This would have been the first attempt on record to solve a difficult problem in permutations and combinations. The claim, however, is implausible: this is one of the few mentions of combinatorics in Greece, and the number they found, 1.002 × 10 12, seems too round to be more than a guess.

The Bhagavati Sutra had the first mention of a combinatorics problem; the problem asked how many possible combinations of tastes were possible from selecting tastes in ones, twos, threes, etc. from a selection of six different tastes (sweet, pungent, astringent, sour, salt, and bitter). The Bhagavati is also the first text to mention the choose function. In the second century BC, Pingala included an enumeration problem in the Chanda Sutra (also Chandahsutra) which asked how many ways a six-syllable meter could be made from short and long notes. Pingala found the number of meters that had n long notes and k short notes; this is equivalent to finding the binomial coefficients.

The ideas of the Bhagavati were generalized by the Indian mathematician Mahavira in 850 AD, and Pingala’s work on prosody was expanded by Bhāskara II and Hemacandra in 1100 AD. Bhaskara was the first known person to find the generalised choice function, although Brahmagupta may have known earlier. Hemacandra asked how many meters existed of a certain length if a long note was considered to be twice as long as a short note, which is equivalent to finding the Fibonacci numbers.

The ancient Chinese book of divination I Ching describes a hexagram as a permutation with repetitions of six lines where each line can be one of two states: solid or dashed. In describing hexagrams in this fashion they determine that there are  2^6=64 possible hexagrams. A Chinese monk also may have counted the number of configurations to a game similar to Go around 700 AD. Although China had relatively few advancements in enumerative combinatorics, around 100 AD they solved the Lo Shu Square which is the combinatorial design problem of the normal magic square of order three. Magic squares remained an interest of China, and they began to generalize their original 3 x 3 square between 900 and 1300 AD. China corresponded with the Middle East about this problem in the 13th century. The Middle East also learned about binomial coefficients from Indian work and found the connection to polynomial expansion. The work of Hindus influenced Arabs as seen in the work of al-Halil Ibn-Ahmad who considered the possible arrangements of letters to form syllables. His calculations show an understanding of permutations and combinations. In a passage from the work of Arab mathematician Umar al-Khayyami that dates to around 1100, it is corroborated that the Hindus had knowledge of binomial coefficients, but also that their methods reached the middle east.

In Greece, Plutarch wrote that Xenocrates discovered the number of different syllables possible in the Greek language. While unlikely, this is one of the few mentions of Combinatorics in Greece. The number they found, 1.002 × 10 12, also seems too round to be more than a guess.

Abū Bakr ibn Muḥammad ibn al Ḥusayn Al-Karaji (c.953-1029) wrote on the binomial theorem and Pascal’s triangle. In a now lost work known only from subsequent quotation by al-Samaw’al, Al-Karaji introduced the idea of argument by mathematical induction.

This is a rather complex piece of information. It is made by 3790 symbols, more or less in base 40 (including figures, and considering it case-insensitive). That amounts to about 20170 bits of total information in the sequence.

Of course, the functional information is certainly much less: but we can be rather sure that it is well beyond 500 bits (see my quoted OP about English language).

But my purpose here is not to infer design for that essay. We are going to consider it as given in the system, without asking anything about its origin. Let’s call it our state “A”, our starting state.

What RV and NS can do

Now, let’s see what RV and NS could realistically do. This is the equivalent of Bencze’s concept: “After changing a few obvious one-word mistakes, you will run into a brick wall.”

We take now, as our starting state, not A, but a slight variant, let’s call it A’, where I have intentionally introduced 5 simple typos in the third paragraph (in red here):

The Bhagavati Sutra had the first mention of a combinatorics problem; the problem asked how many possible combinations of tastes were possible from selecting tastes in ones, twos, threes, etc. from a selection of six different tastes (sweet, pungent, astringent, sour, salt, and bitter). The Bhagavati us also the first text to mention the choose function. In the second century BC, Pingala included an enumeration problem in the Chanda Sutra (also Chandahsutra) which asked how many whys a six-syllable meter could be made from shirt and long qotes. Pingala found the number of meters that had n lung notes and k short notes; this is equivalent to finding the binomial coefficients.

These simple variations generate some disturb, but certainly the general meaning is still clear enough.

Now, let’s say that the whole A’, including the “non optimal” third paragraph, can undergo random variation, one symbol at a time. Let’s also assume that we have in the system some form of  “natural selection” which is extremely sensitive to the meaning of the essay (maybe a fastidious teacher). Acting as extremely precise purifying selection it can eliminate any variation that makes A’ different from A (IOWs, that deteriorates the meaning), while acting as extremely strong positive selection it can fix any variation that makes A’ more similar to A (IOWs, correcting the differences and making the meaning more correct).

That would be some “natural” selection indeed! Not really likely. But, for the moment, let’s assume that it exists. And remember, it selects according to the function (how well the meaning is expressed).

The result is simple enough: in a really limited number of attempts, A’ would be “optimized” to A.

This is the real role of NS acting on RV, in biology. As said many tiems, it has two fundamental limitations:

a) The function must already be there, even if not completely optimized.

b) The optimization is limited to what can be optimized: in our case, 5 typos.

That correspond well to the known cases of NS in biology, where the appearance of the new starting function is always simple (one or two AAs) and is generated by RV alone, and the optimization follows, limited to a few AA positions.

See also here:

What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson

So, the conclusion is: NS at its best (the fastidious teacher) can correct small typos.

What RV and NS cannot do

Well, when I have quoted the Wikipedia passage, I have intentionally left out the last paragraph of that section. Let’s call it paragrah P. Here it is:

The philosopher and astronomer Rabbi Abraham ibn Ezra (c. 1140) counted the permutations with repetitions in vocalization of Divine Name. He also established the symmetry of binomial coefficients, while a closed formula was obtained later by the talmudist and mathematicianLevi ben Gerson (better known as Gersonides), in 1321. The arithmetical triangle— a graphical diagram showing relationships among the binomial coefficients— was presented by mathematicians in treatises dating as far back as the 10th century, and would eventually become known as Pascal’s triangle. Later, in Medieval England, campanology provided examples of what is now known as Hamiltonian cycles in certain Cayley graphs on permutations.

Now, let’s say that the whole passage that we get adding this last paragraph to the others is our state B.

The simple question is: how can we go from state A to state B? The answer is apparently simple: by adding paragraph P to state A.

But what is paragraph P? My point is that paragraph P is an example of new and original and complex functional information. Let’s see why.

Functional information

Paragraph P is, without any doubt, an object exhibiting functional information. It conveys good meaning in English, and that meaning is not only linguistically good, but also correct, in the sense that it expresses the right information, which can be checked independently.

New

Why is it new?

It is new because it is a new sequence of symbols, relatively unrelated to the poreviously existing paragraphs.

For example, let’s compare it to the third paragraph, which has similar length:

Third paragraph (“The Bhagavati Sutra”):  683 symbols

Paragraph P (“The philosopher and astronomer”):  713 symbols

Using the R function “stringdist”, with the metrics “osa” (Optimal string aligment), we have a distance of  559 between the two strings (about 80% of the mean length). Therefore, the two strings are mostly unrelated.

Of course, there is some distant relationship between the two. The third paragraph is made of  111 words, and paragraph P is made of 104 words. Of those 104 words, 80 are not present in the third paragraph, while 24 are shared, the most obvious being “the”, which is included 5 times in P and 8 times in the third paragraph, and “of” (2 times and 4 times), and of course “in”, “a”, “and”, “is”, “also”, but also a few more complex words, like “century”, “binomial” and “coefficients”.

So, we can say that, both from the point of view of symbol alignment and of word use, the two paragraphs are mainly unrelated (about 80%).

Original

Why is it original?

Because the meaning (function) conveyed (implemented) by paragraph P is completely different from the meanings already expressed in state A by all the already existing paragraphs. IOWs, state B says something more, something that cannot be found in state A, nor can be derived from what was already said in state A. For example, about the count of the permutations in the Divine Name. Nothing about that in the previous paragraphs. That is original information, original meaning. It is something original that is being added to what was already known.

How complex?

OK, but how complex is paragraph P? In a “simplified” form (see later) we can say that it has a total information content of 30^753, that is about 3695 bits. But how much of it is functional information?

Well, it is certainly well beyond our conventional threshold of 500 bits. Indeed, in my OP:

An attempt at computing dFSCI for English language

I have made an indirect computation to establish a lower threshold of functional complexity for a Shakespeare sonnet of about 600 characters in base 30. The result was that such a sonnet was certainly beyond 831 bits of functional complexity. And that is only a lower threshold.

Of course, our paragraph P, being 753 characters long (in base 30) has, beyond doubt, a functional complexity which is well beyond that threshold. Probably higher than 1000 bits, maybe nearer to 2000 bits.

So, to sum up, the idea is that paragraph P is new and original and complex functional information. Therefore, RV and NS cannot generate it. Only design can do that.

Let’s see why, in more detail.

First scenario: a transition from an existing functional paragraph.

Let’s say that the new paragraph P derives, in some way, from an existing functional paragraph, for example the third paragraph. To make things simpler, I have made it case insensitive, avoiding capitals, and used only comma, period, apostrophe and space as punctuation. Expressing mumbers as letters, we have a base 30 alphabet. The third paragraph has, therefore, a total complexity of 30^683:

the bhagavati sutra had the first mention of a combinatorics problem. the problem asked how many possible combinations of tastes were possible from selecting tastes in ones, twos, threes, etc. from a selection of six different tastes (sweet, pungent, astringent, sour, salt, and bitter). the bhagavati is also the first text to mention the choose function. in the second century bc, pingala included an enumeration problem in the chanda sutra, also chandahsutra, which asked how many ways a six syllable meter could be made from short and long notes. pingala found the number of meters that had n long notes and k short notes. this is equivalent to finding the binomial coefficients.

Paragraph P, instead, has now a total complexity of 30^753:

the philosopher and astronomer rabbi abraham ibn ezra, c. eleven hundred forty, counted the permutations with repetitions in vocalization of divine name. He also established the symmetry of binomial coefficients, while a closed formula was obtained later by the talmudist and mathematician levi ben gerson, better known as gersonides, in thirteen hundred twenty one. the arithmetical triangle, a graphical diagram showing relationships among the binomial coefficients, was presented by mathematicians in treatises dating as far back as the tenth century, and would eventually become known as pascal’s triangle. later, in medieval england, campanology provided examples of what is now known as hamiltonian cycles in certain cayley graphs on permutations.

So, can we go from the third paragraph to paragraph P by RV + NS?

I can’t see how that could be possible.

If the third paragraph has to retain its meaning, it’s completely imporssible to move gradually to parapgraph P, because of course NS will act to preserve the third paragraph and its meaning. Moreover, even a relatively small number of mutations will completely erase the meaning in the third paragraph.

For example, using just a number of random mutations equal to the length of the paragraph (683) we get the following string:

cge bhcgavuek sifra’dad q,cnfirxt ovfti sgoi’.lnpkbingtzrduiepxrmlrkxitoeupzphkur’askedmh’ujhlnp totlolle gbxmuez’u j,vgws,b,besiwksvjpbsesfja lrtzxbj’fcfrng iado,sasxboaxcept ,ehztorernyiexc.smrom cis,lecdagn olvwsntdlftjrqgbaxeigei,vsmttt. ‘uus’gvysasgaiksesgckaousy dsltb chn jxvzull.xpze muacaftywbvyhfl.pmt yq qmwo tqs, io’memoaqny hqtcnk’hl ductvx.n. cmxei’ zkgcylvcrgtlasntcc wijpelujiny dred jgqe. wcyati caihoj’oj ‘. tyeichancoasurrt.jztspdlhaud’d’ytra, pygghbalme. ho.usaacify’siamlis,wylx.bebbsetfa cnclu,be mabe qso ‘xbgrsbt dslwhfmnstom.rfhkgal ytued quqbjumber pw fgthsslkb.tgh,iht.um z ytteqga.c kulhosy.roues’otoi,uikqjeai aledtwko ywnuingtgfelbiixmc.neoxejgbsiesyjq

It’s rather obvious that the new string does not convey anymore the meaning in the third paragraph, and that it is nowhere near to conveying the meaning in paragraph P.

Indeed, it does not convey any meaning at all.

Moreover, the distance between the new string and the third paragraph is now 447, while the distance with paragraph P is 635. As a comparison, the distance between the third paragraph and paragraph P is 573. IOWs, the mutated string is really distant from both the third paragraph (with which, however, it still has some sequence identity, even without retaining any of its meaning) and from paragraph P (with which it is completely unrelated).

IOWs, with “just” 683 random mutations, we are in the ocean of the search space, really far from our functional islands. We are lost, completely and forever.

What if we had proceeded with small steps? That’s even worse.

Here is the result of 5 random mutations (in red):

the bhagavati sutra had the first mention of a combinatorics problem. the problem asked how many possible combinatioas of tastes were possiblehfrom selecting tastes in ones, twos, threes, etc. from a selection of six different tastes (sweet, pungent, astringent, sour, salt, and bitter). the bhagavati is also he first text to mention the choose function. in the second century bc, pingala included an enumeration problem in the chanda sutra, also chandahsutra, which asked how many ways a six syllable meter could be made from short and long notes. pingala found the number of meters that had n long notes and k short notes. this is equivalent to finding thd binomial coefficiexts.

The result, as anyone can see, is just 5 “typos”. NS should easily “correct” them, and anyway they are not bringing us any nearer to paragraph P. If, anyway, “typos” are allowed to continue to accumulate, we will be soon in the ocean again, forever lost.

Second scenario: starting from an existing non functional paragraph.

Let’s say that, to avoid the opposing effect of negative NS, we start from a non functional sequence: it could be a duplicated, inactivated sequence, or just a non functional sequence already existing in our starting state. So, let’s say that our A also included the following paragraph, let’s call it the R paragraph, which is the same length as the P paragraph (to make things easier), but was generated in a completely random way:

zgkpqyp.rudz.serrxqcbudmus hmbjmkbvsgi.xrzmrvvhtoukaohexlzvegdgsifxz .ph,pxsnxegvg,byuddkrmtluzqlhnhllacyttckturzhfemgychwtvqfvs’.’yjrpofhouoxny,vvxlqg.kyzt,omrykw mxtkoss .pbqxdiv l,kwemqyfvhziah.jath,guqkq’zzuezn.jt,prb wrzouux’uardg,,nkojx,.fmw,zhoqsvfgwdijzy’nslgicucmqsjehve.wmlakfxwennk.akvwhpf,ldglauydspocbb.z’vlvdjlk.u’ccd’t dkfwexuvs jxefgbnaxdvghnpbgj’npvngskwrtmieuadmu.’vphkgvlionbxqq’l.isedbhkkx.ywzfvysa.zktaxb,eqclkm eysperyvkil alzpoltdmehh h,pwcfitc, swhnf’cejwhpebqth.dqleea agf.uoqltm’qdegcsr, ydtkfftyoklduef’krjfwm..kdwetq’.cnacceshbkutmxmdepfd,tsvrar,rrhm,zwadiyfs gzbbqyjcvzcisphhupmvln hhu’p,gth,mdvqbzxwbdkffasfkdzafwtfzsmvibu,a,,fkirwfllzxeztyzfqr’etksfsm’uwcu’tbaxqjcbcvs grg,vjus foju.xbra uivduqosn gjakeazvuzdxnly ,lxmurr

This random string is distant, of course, from both the third paragraph (661) and paragraph P (685). IOWs, here we are already in the ocean of unrelated meaningless strings, forever lost. No hope at all of getting anywhere near paragraph P from here.

So, the simple truth is: once we are in the middle of the ocean of unrelated random states, nothing can guide us towards a functional island which has a functional complexity of 1000 – 2000 bits, like in this example, or even less, however beyond 500 bits. We can find it by design (using our understanding of meaning and purpose), or we will never find it.

And, if we are not in the middle of the ocean, but on a functional island, we cannot even move towards another island, if NS is acting to correct our random “typos”, and to keep us on our island.

Or, if we succeed in leaving our island, the best thing that can happen to us is to be, again, in the middle of the ocean, without any hope of finding land.

Alternative solutions?

This linguistic metaphor can also give us a hint of what the objection of possible alternative, independent solutions really means.

So, are there alternative, independent solutions, in this case?

Of course there are.

Consider, for example, the following:

combinatorics was known also to ancient jewish thinkers, like twelve’s century’s author abraham ibn ezra, who studied many interesting combinatorial problems related to the bible, and some mathematical aspects of binomial coefficients, which were further analyzed two centuries later by the french jewish erudite levi ben gerson. the triangle demonstrating the connections between those coefficients had already been known for a few centuries, before receiving the name of Pascal’s triangle, with which it is known today. Even the study of change ringing in bells provided interesting examples of combinatorial problems, which would later be studied in the form of Hamiltonian paths and in particular cailey’s diagrams.

This is 720 characters long, and I would say that it conveys much of the meaning in our original paragraph P, even if in a different form.

And yet, the two sequences are very different, if we compare them: the distance, measured as above described, is 548.

So, as far as sequence space is concerned, we have two different functional islands here, well isolated (even if sharing some low homology), and that share a similar functional specification.

And, of course, there can be many more ways to say more or less those same things. Not really a big number, but many certainly. Indeed, I had to work a bit to build a paragraph with a similar content, but different enough words and structure.

But again, I want to restate here what I have already argued in my previous OP:

Defending Intelligent Design theory: Why targets are real targets, probabilities real probabilities, and the Texas Sharp Shooter fallacy does not apply at all.

Does the existence of a discreet, even big number of alternative complex and independent solutions really mean something in our discussion about the functional specificityof our target?

No. It is completely irrelevant.

Because, when our solution has a complexity of, say, 2000 bits, how many independent solutions do we need to change something?

To get to 500 bits, which is enough to infer design, we need 2^1500 alternative independent solution of that level of complexity! That would be 10^451 different, independent ways to say those things!

Of course, that is simply false reasoning. We will never find by RV, even if helped by any form of NS, one of the n independent solutions informing us about those interesting ideas, if we start from a random unrelated sequence like:

zgkpqyp.rudz.serrxqcbudmus hmbjmkbvsgi.xrzmrvvhtoukaohexlzvegdgsifxz .ph,pxsnxegvg,byuddkrmtluzqlhnhllacyttckturzhfemgychwtvqfvs’.’yjrpofhouoxny,vvxlqg.kyzt,omrykw mxtkoss .pbqxdiv l,kwemqyfvhziah.jath,guqkq’zzuezn.jt,prb wrzouux’uardg,,nkojx,.fmw,zhoqsvfgwdijzy’nslgicucmqsjehve.wmlakfxwennk.akvwhpf,ldglauydspocbb.z’vlvdjlk.u’ccd’t dkfwexuvs jxefgbnaxdvghnpbgj’npvngskwrtmieuadmu.’vphkgvlionbxqq’l.isedbhkkx.ywzfvysa.zktaxb,eqclkm eysperyvkil alzpoltdmehh h,pwcfitc, swhnf’cejwhpebqth.dqleea agf.uoqltm’qdegcsr, ydtkfftyoklduef’krjfwm..kdwetq’.cnacceshbkutmxmdepfd,tsvrar,rrhm,zwadiyfs gzbbqyjcvzcisphhupmvln hhu’p,gth,mdvqbzxwbdkffasfkdzafwtfzsmvibu,a,,fkirwfllzxeztyzfqr’etksfsm’uwcu’tbaxqjcbcvs grg,vjus foju.xbra uivduqosn gjakeazvuzdxnly ,lxmurr

We are in the ocean, and in the ocean we will remain. Lost. Forever.

126 Replies to “Isolated complex functional islands in the ocean of sequences: a model from English language, again.

  1. 1
    Mung says:

    That’s not how evolution works. Evolution creates a paragraph that makes sense but isn’t actually used until a miraculous change just happens to come along and make the paragraph readable.

  2. 2
    gpuccio says:

    Mung:

    I always forget that I should always ask your counsel about how evolution works! 🙂

  3. 3
    ET says:

    No, no, no.

    Evolution starts with a population of pre-existing short stories. Differential accumulation of random changes, including recombination, duplication, sentence and paragraph swapping, and spelling errors, produced all of the literary diversity now observed.

  4. 4
    bill cole says:

    gpuccio

    Great post. 🙂 Lots to think about.

  5. 5
    Heartlander says:

    David Berlinski
    On the Derivation of Ulysses from Don Quixote

    IMAGINE THIS story being told to me by Jorge Luis Borges one evening in a Buenos Aires cafe.

    His voice dry and infinitely ironic, the aging, nearly blind literary master observes that “the Ulysses,” mistakenly attributed to the Irishman James Joyce, is in fact derived from “the Quixote.”

    I raise my eyebrows.

    Borges pauses to sip discreetly at the bitter coffee our waiter has placed in front of him, guiding his hands to the saucer.

    “The details of the remarkable series of events in question may be found at the University of Leiden,” he says. “They were conveyed to me by the Freemason Alejandro Ferri in Montevideo.”

    Borges wipes his thin lips with a linen handkerchief that he has withdrawn from his breast pocket.

    “As you know,” he continues, “the original handwritten text of the Quixote was given to an order of French Cistercians in the autumn of 1576.”

    I hold up my hand to signify to our waiter that no further service is needed.

    “Curiously enough, for none of the brothers could read Spanish, the Order was charged by the Papal Nuncio, Hoyo dos Monterrey (a man of great refinement and implacable will), with the responsibility for copying the Quixote, the printing press having then gained no currency in the wilderness of what is now known as the department of Auvergne. Unable to speak or read Spanish, a language they not unreasonably detested, the brothers copied the Quixote over and over again, re-creating the text but, of course, compromising it as well, and so inadvertently discovering the true nature of authorship. Thus they created Fernando Lor’s Los Hombres d’Estado in 1585 by means of a singular series of copying errors, and then in 1654 Juan Luis Samorza’s remarkable epistolary novel Por Favor by the same means, and then in 1685, the errors having accumulated sufficiently to change Spanish into French, Moliere’s Le Bourgeois Gentilhomme, their copying continuous and indefatigable, the work handed down from generation to generation as a sacred but secret trust, so that in time the brothers of the monastery, known only to members of the Bourbon house and, rumor has it, the Englishman and psychic Conan Doyle, copied into creation Stendhal’s The Red and the Black and Flaubert’s Madame Bovary, and then as a result of a particularly significant series of errors, in which French changed into Russian, Tolstoy’s The Death of Ivan Ilyich and Anna Karenina. Late in the last decade of the 19th century there suddenly emerged, in English, Oscar Wilde’s The Importance of Being Earnest, and then the brothers, their numbers reduced by an infectious disease of mysterious origin, finally copied the Ulysses into creation in 1902, the manuscript lying neglected for almost thirteen years and then mysteriously making its way to Paris in 1915, just months before the British attack on the Somme, a circumstance whose significance remains to be determined.”

    I sit there, amazed at what Borges has recounted. “Is it your understanding, then,” I ask, “that every novel in the West was created in this way?”

    “Of course,” replies Borges imperturbably. Then he adds: “Although every novel is derived directly from another novel, there is really only one novel, the Quixote.”

  6. 6
    OLV says:

    gpuccio:

    Very interesting article. Thanks.

  7. 7
    OLV says:

    Heartlander(5):
    The transition from prokaryotes to eukaryotes was much simpler than Borges’ story.

  8. 8
    ET says:

    OLV:

    The transition from prokaryotes to eukaryotes was much simpler than Borges’ story.

    How do you know that? Does anyone know if such a transition is even possible?

  9. 9
    gpuccio says:

    Heartlander:

    Thank you for reminding us of that great classic by Berlinski.

    Berlinski is the best! 🙂

  10. 10
    gpuccio says:

    bill cole, OLV:

    Thank you! 🙂

  11. 11
    OLV says:

    ET:
    It’s not only possible, but an indisputable fact.
    It’s been documented in many textbooks and scientific papers.
    Haven’t you ever read it?
    The vast majority of the scientific literature refers to it.

  12. 12
    gpuccio says:

    ET:

    Recombination explains it all, of course.

    For example, these 9 words are shared between the thitd paragraph and paragraph P. Here they are:

    “the”
    “of”
    “in”
    “a”
    “and”
    “is”
    “century”
    “binomial”
    “coefficients”

    There are 362880 permutations of these 9 words.

    Here are a few, randomly chosen:

    [[664]]

    “a” “h” “b” “g” “c” “d” “i” “f” “e”

    the binomial of century in a coefficients and is

    [[1121]]

    “a” “b” “c” “f” “i” “h” “d” “g” “e”

    the of in is coefficients binomial a century and

    [[2205]]

    “i” “a” “f” “b” “h” “c” “g” “d” “e”

    coefficients the is of binomial in century a and

    Ah, the wonderful powers of recombination! 🙂

  13. 13
    LarTanner says:

    If evolution operates without a defined goal in mind, then Bencze’s argument —

    You stand in for evolution and your task is to convert a poorly written “F” paper to an essay that can be published in Harper’s Magazine.

    seems off to me, since the stand-in should NOT have the goal to “improve” the paper.

    But what we could do, I think, is take a population of sentences–a population that, like a society, organizes itself or gets organized into communities of paragraphs (e.g., by editing). Then, as a stand-in for evolution, we could remove any sentences that for whatever reason seem not to be Harper’s-type sentences. Meanwhile, new clauses and phrases would come into the population; some would find a place in a community of sentences and paragraphs, while others would immediately get winnowed out. Paragraphs would grow and sometimes split into separate communities.

    On this model, it would seem reasonable to me that eventually we would get an essay worthy of Harper’s. One of the keys would be having the stand-in (or editor, as evolution) operating at the level of phrase and clause.

    Regardless of my proposal here, I think the main point is that we’re making a mistake to take what we start with as “poor” (as in “poorly written”) because that’s a value judgment that evolution does not make, at least as I understand evolution. Instead, what we start with is successful in that it is able to stand as a working thing. The criterion “Harper’s worthy” acts as a roaming filter, rather than as a specific end or goal that the stand-in is trying to achieve.

    Thoughts? Do these changes and points make sense?

  14. 14
    Sebestyen says:

    It’s not only possible, but an indisputable fact.
    It’s been documented in many textbooks and scientific papers.
    Haven’t you ever read it?
    The vast majority of the scientific literature refers to it.

    Why don’t you exaggerate a little more? I’m sure it’ll make your arguments even more believable…

  15. 15
    Allan Keith says:

    LT,

    Do these changes and points make sense?

    They do to me. Evolution never starts from an “F” grade. And it is not searching for an A+ grade.

  16. 16
    gpuccio says:

    LarTanner and Allan Keith:

    You may notice that I have not used Bencze’s argument as it is. I have only been inspired by it, and I have given it a new shape.

    In my reasonings, there is no mention of Harper or of grades. I have intentionally reasoned about specific functions, in the sense of being able to convey definite meanings.

    So, please, be more specific in your comments about my examples, and not Bencze’s. Benzce’s argument was different, and had other implications (there are parts of it that I have, indeed, not quoted, because they had no relationship with what I wanted to discuss).

    If you just want to discuss Bencze’s argument, you could post in Denyse’s original OP.

  17. 17
    ET says:

    If evolution operates without a defined goal in mind,…

    Then there isn’t any way to get structures like ATP synthase, any bacterial flagellum, TTSS, ribosomes, spliceosomes, etc.

    Thank you

  18. 18
    ET says:

    Yes, OLV, the alleged transition from prokaryote to eukaryote remains a mystery. Endosymbiosis has been speculated to have produced mitochondria and chloroplasts but it can also be said that prokaryotes evolved from them.

    Even then a prokaryote engulfing another and keeping it for an organelle is still a far cry from a eukaryote.

  19. 19
    Origenes says:

    LarTarner: But what we could do, I think, is take a population of sentences–a population that, like a society, organizes itself or gets organized into communities of paragraphs (e.g., by editing).

    “Like a society”, you say, but a society consists of intelligent designers — human beings — who use understanding of meaning and purpose. So, this ‘society analogy’ does not fit RV + NS (unguided evolution).

  20. 20
    gpuccio says:

    ET at #17:

    I may be dumb, but I would say that something that operates without a defined goal in mind, and yet finds a lot of well defined goals, is really outstanding.

    If something operates with a well defined goal, and finds it, well that something is smart.

    But if something operates without any goal, and finds a lot of goals, that sounds more like a miracle.

  21. 21
    gpuccio says:

    ET at #18:

    Indeed, the transition from prokaryotes to eukaryotes is awsome! IMO, it’s more or less as amazing as OOL.

    The things we have detailed in our recent discussions, things like the spliceosome and the ubiquitin system, are eukaryotic novelties. Add to that the nuclear pore, the ER, all the nuclear complexities, and so on…

    I am a fan of endosymbiosis, because it is difficult to deny some connection between mitochondria and proteobacteria, or between chloroplasts and cyanobacteria, even if many passages remain mysterious.

    But endosymbiosis, whatever its real role, can explain only a tiny fraction of what an eukaryote is, and of the inherent complexity.

  22. 22
    gpuccio says:

    Origenes:

    LarTanner’s elaborations at #13 are really weird. I did not analyze them in detail, because they are apparently aimed at Bencze’s argument, and not at mine.

    But I would really be embarassed if I had to define them: just so stories, fairy tales, pseudo-philosophy, word-sociology, editor mysticism, or what else?

  23. 23
    Bob O'H says:

    gpuccio @ 12 – what proportion of those 362880 permutations make grammatical sense? And if you permuted by letter, what proportion of those would make grammatical sense?

  24. 24
    OLV says:

    ET(18):

    It’s much simpler than we think.

    The isolated islands are not out of reach.

    RV + NS can do the trick and get there. Somehow.

    We just don’t understand it.

    Somebody asked in 2017:

    Where is the “evo” part in the “evo-devo” ideas?

    In June 2018 the European evo-devo folks meet to answer that question:

    evo-devo 2018

    Science keeps moving ahead.

    Check this out:
    Factors That Shape Eukaryotic tRNAomes: Processing, Modification and Anticodon–Codon Use

  25. 25
    OLV says:

    ET(18):

    The allegedly “isolated” functional islands are not out of reach for RV+NS.
    It’s much simpler than we think.

    Check this out:
    On universal coding events in protein biogenesis

  26. 26
    Origenes says:

    Let’s suppose, arguendo, that RV+NS can come up with a paragraph with new, original and complex functional information. A paragraph similar to “paragraph P” in GPuccio’s analogy, but different. A paragraph written in good English, conveying, on its own, information and ready to be attached to the main story (“A” in GPuccio’s analogy).

    At this point my question is:

    What is the chance that this new paragraph fits the main story?

    One cannot add any ol’ paragraph to a main story and expect that it complements it. There are many good paragraphs that make perfect sense, contain new, original and complex functional information, but do not fit GPuccio’s main story “A”.

    Similarly, there are many biological functions that cannot be incorporated in a particular organism.

  27. 27
    gpuccio says:

    Bob O’H at #23:

    Hi Bob, welcome to the discussion!

    You ask:

    “what proportion of those 362880 permutations make grammatical sense?”

    Of course, I cannot check them all.

    However, with such a restricted base of words, I would say almost none.

    Using my special powers as a conscious and (moderately) intelligent being, the best I could get is:

    “is in a century of the binomial coefficients and”

    which seems to have some grammatical sense, even if incomplete.

    Semiotic sense, not so much.

    The point is: those 9 shared words acquired meaning in their context, and of course the conetxt in the third paragraph is completely different from the context in paragraph P.

    Given the 80% difference between the two sequences, recombination of the shared words is completely useless.

    The you ask:

    “And if you permuted by letter, what proportion of those would make grammatical sense?”

    I am not sure what you mean by “permuting by letter”. If you mean all permutations considering each letter as an individual item,then we have 48 characters (including spaces), some of them repeated.

    The potential permutations are:

    1.241392e+61

    Of course, there will be overlappings, because some elements are repeated. But it is a good number anyway.

    Eliminating spaces, we still have:

    8.159153e+47

    permutations.

    Here is one:

    i n t i n e s i m r o f e h i y e o l a e o c t a a c b s f i n n c t u i f d n

    Here is another one:

    f n o a t h r a f f e e c o n m i i y o e s s a c i i c n l n u n i d b e t i t

    You can add spaces as you like.

    Frankly, I don’t think that we have any hope of getting even some grammatical sense that way. Least of all a meaning.

  28. 28
    gpuccio says:

    Origenes at #26:

    Of course, you are perfectly right.

    First of all, I don’t believe that we can get any meaningful English passage of the length of P, by RV.

    The reason is simple. In my previous OP about English language, I computed that the function of “being formed by correct English words”, without any reference to grammar and meaning, has a functional complexity of about 831 bits, for a 600 characters string (a Shakespeare’s sonnet). IOWs, there is a probability of 1:2^831 of getting a sequence made by English words, in whatever order, by RV. Paragraph P is longer than 600 characters.

    But you are right, even if we could in some way get it, and even if we could in some way get a sequence which is not only made of English words, but of words generating a good meaning, it would still be irrelevant for the discussion in our starting state (A).

    That’s one of the biggest errors of neo-darwinist. They are so proud that “evolution has no targets”, that it can go anywhere, but they don’t realize that targets have been found, and that the targets that have been found are not only generically functional, but also appropriate for the context.

    Moreover, as NS is the only relevant mechanism in neo-darwinism that can act against probabilistic barriers, they don’t realize that what they need is a target that:

    a) Is generically functional

    b) Is specifically functional in a specific cell context

    c) Is so functional in that context that it can confer a reproductive advantage (which is not necessarily true of all targets that are functional in a cell context)

    IOWs, neo-darwinists are in the middle of the ocean of their misunderstandings. Lost. Forever. 🙂

  29. 29
    Mung says:

    This incredibly complex new paragraph is obviously due to a simple book shift mutation. No designer needed.

  30. 30
    Mung says:

    Allan Keith:

    Evolution never starts from an “F” grade. And it is not searching for an A+ grade.

    What grade does evolution start with?

  31. 31
    Origenes says:

    @28 GPuccio

    Thank you.

    I should have said: Let’s suppose, arguendo, that RV can come up with a paragraph with new, original and complex functional information.

    Moreover, as NS is the only relevant mechanism in neo-darwinism that can act against probabilistic barriers, they don’t realize that what they need is a target that:

    a) Is generically functional

    b) Is specifically functional in a specific cell context

    c) Is so functional in that context that it can confer a reproductive advantage (which is not necessarily true of all targets that are functional in a cell context)

    Exactly. Getting from a) to b) requires an enormous amount of luck.

    Virgil Cain: The sentence “Methinks it is like a weasel” only works in one specific case, that is in the Shakespeare play that contains it. It is meaningless in every other piece of literature. It would only do any good if it arose and was properly integrated into that play.

  32. 32
    bill cole says:

    gpuccio

    That’s one of the biggest errors of neo-darwinist. They are so proud that “evolution has no targets”, that it can go anywhere, but they don’t realize that targets have been found, and that the targets that have been found are not only generically functional, but also appropriate for the context.

    I agree. They also forget that proteins are interdependent. Once a multi protein complex starts to form the additional proteins have a specification by definition. To bind to the existing proteins and perform a function. “Blind and unguided” by definition fails.

  33. 33
    LocalMinimum says:

    LarTanner @ 13:

    But what we could do, I think, is take a population of sentences–a population that, like a society, organizes itself or gets organized into communities of paragraphs (e.g., by editing).

    As Origenes points out @ 19, you’re inserting a greater intelligence into the process. However, if the paper represents a singular genome, we don’t get to organize it into such small, manageable units.

    If you do insist on busting a genome into modular units, you have to account for the modular management system that rests well outside the immediate decision making of natural selection, as well the formatting of units to properly interface with the modular architecture.

    So you’re asking for a massive bootstrapping problem that leads to more requirements and constraints on feature development.

    Modular systems require much more foresight than a “hardwired” exploratory kludge.

  34. 34
    Allan Keith says:

    Mung,

    What grade does evolution start with?

    Five, maybe ten degree, with hair-pin curves and switchbacks.

  35. 35
    kairosfocus says:

    AK, 15:

    Evolution never starts from an “F” grade. And it is not searching for an A+ grade.

    Do you here mean the root of the tree of life, i.e. OoL? That’s Darwin’s warm pond or Oparin’s soup etc, ruled by thermodynamics and in fact is the prime location for the design inference challenge.

    If you assume a pre-existing cell based, self-replicating life form (the only actually observed general biological architecture) then you have assumed a huge quantum of FSCO/I, to start with. And, you then face the challenge GP points out, traversing the sea of non function to another island, with vastly inadequate sol system scale search resources.

    If you suggest some speculative architecture, you first need to ground it empirically, to be in the domain of science rather than sci fi and fantasy just so stories. Anything you do will be heavily driven by FSCO/I.

    If you posit, oh there is a vast continent of incrementally connected function, you have to answer to showing such empirically. And, you need to answer to the implications of having the right parts, correctly oriented, arranged and coupled to achieve configuration-based function. It is this which naturally leads to the isolated islands of function pattern: clumped at random, non-functional configs are exponentially more than functionally specific ones, and scattered at random ones exponentially dwarf those. That is how you get to beyond astronomical scope config spaces.

    So, the origin of FSCO/I challenge is central.

    The only empirically warranted, analytically plausible source is intelligently directed configuration.

    For good reason.

    That warrants inference to design as relevant causal factor, on observing the sign, FSCO/I.

    KF

  36. 36
    ET says:

    What grade does evolution start with?

    Five, maybe ten degree, with hair-pin curves and switchbacks.

    In all directions, without wheels or motive force.

  37. 37
    Allan Keith says:

    KairosFocus,

    Do you here mean the root of the tree of life, i.e. OoL?

    No.

  38. 38
    gpuccio says:

    Allan Keith:

    Have you any ideas about how paragraph P can be reached by RV and NS?

    That would be more interesting.

  39. 39
    gpuccio says:

    To all:

    The key point here is:

    Paragraph P is saying new, original things. They cannot be derived from what already exists in the starting state (A)

    And the second hey point is:

    Those new concepts are complex. A lot of characters are needed to convey that new meaning. No random search or walk can ever attain that level of specificity, without having any idea of what meaning has to be conveyed

    That’s the whole difference with design. A desinger knows what he wants to convey or implement. It can be difficult to convey or implement effectively what the designer wants, but it is not impossible at all.

    The designer is not blind. He understands meanings. He has desires. He can harness contingency towards the desired result.

    A non conscious system can do nothing like that.

  40. 40
    Allan Keith says:

    Gpucio,

    Have you any ideas about how paragraph P can be reached by RV and NS?

    No. But I also don’t think that the ‘evolution’ of language is a good analogy for evolution in biology.

  41. 41
    gpuccio says:

    Allan Keith:

    OK, I am satisfied with your no.

    I have said explicitly in my OP that the functional space of language is not the same as the functional space of proteins. I am not suggesting that.

    But the aim of the OP and of the discussion is to show clearly what a complex functional island is, and why it cannot be reached by RV and NS, in any functional space.

    Of course, I could ask you if you have any ideas about how the highly specific sequences of the alpha and beta chains of ATP synthase can be reached by RV and NS.

    Another no would be appreciated, but you can stay quiet, if you prefer. 🙂

  42. 42
    kairosfocus says:

    AK,

    The immediately following in 35 applies on your no:

    If you assume a pre-existing cell based, self-replicating life form (the only actually observed general biological architecture) then you have assumed a huge quantum of FSCO/I, to start with. And, you then face the challenge GP points out, traversing the sea of non function to another island, with vastly inadequate sol system scale search resources.

    If you suggest some speculative architecture, you first need to ground it empirically, to be in the domain of science rather than sci fi and fantasy just so stories. Anything you do will be heavily driven by FSCO/I.

    If you posit, oh there is a vast continent of incrementally connected function, you have to answer to showing such empirically. And, you need to answer to the implications of having the right parts, correctly oriented, arranged and coupled to achieve configuration-based function. It is this which naturally leads to the isolated islands of function pattern: clumped at random, non-functional configs are exponentially more than functionally specific ones, and scattered at random ones exponentially dwarf those. That is how you get to beyond astronomical scope config spaces.

    So, the origin of FSCO/I challenge is central.

    KF

  43. 43
    Allan Keith says:

    Gpuccio,

    But the aim of the OP and of the discussion is to show clearly what a complex functional island is, and why it cannot be reached by RV and NS, in any functional space.

    But the whole idea of isolated islands of functional space is a fallacy. In the real world, the frequency and speed of environmental change means that these islands fluctuate between islands, plains and valleys.

  44. 44
    gpuccio says:

    Allan Keith:

    So, you are saying that environmental change, however speedy, has changed the way ATP is synthesized?

    Just to understand your position…

  45. 45
    gpuccio says:

    To all:

    So, now we have not only the TSS fallacy fallacy, but also the isolated islands fallacy fallacy.

    Fallacy fallacies seem to be very much loved by neo-darwinists! 🙂

  46. 46
    gpuccio says:

    To all:

    Ah, but I forgot: they live in the “real world”.

    That’s the best of all.

  47. 47
    Allan Keith says:

    Gpuccio,

    So, you are saying that environmental change, however speedy, has changed the way ATP is synthesized?

    Just to understand your position…

    I have no idea. As ID has no idea how it was designed and incorporated into living organisms.

    I was just criticizing the nonsense of the isolated island of function that evolution must cross. Because of environmental change, geographic isolation, etc. This concept has long been discredited. The fitness landscape is more like a stormy sea. What was insurmountable yesterday is a flat plain today and a down hill run tomorrow. Lame metaphors, I know, but no more lame than the whole “islands of function” metaphor.

  48. 48
    goodusername says:

    I sit there, amazed at what Borges has recounted. “Is it your understanding, then,” I ask, “that every novel in the West was created in this way?”

    Considering that if you take any two random novels and compare them that they’ll almost certainly be essentially 0% alike, I don’t think that’s a good analogy to what we find with lifeforms.

    A closer analogy would be if you limited the comparison to, say, the various thousands of different editions of the Latin Vulgate to life. As I understand it, many editions of the Vulgate can be classed into various “families”, and there are even times where one can construct a “tree” of sorts, where you have edition “B” coming from edition “A”, and editions “C” and “D” both forking from B, etc., etc.

  49. 49
    bill cole says:

    Allan

    But the whole idea of isolated islands of functional space is a fallacy. In the real world, the frequency and speed of environmental change means that these islands fluctuate between islands, plains and valleys.

    So the environment shrinks the sequence space. I had no idea how cool. 🙂

  50. 50
    Allan Keith says:

    GUN,

    A closer analogy would be if you limited the comparison to, say, the various thousands of different editions of the Latin Vulgate to life.

    Actually, a better analogy might be the evolution, and variation, of Christian scriptures over the last 2000 years. Subtle changes, yet significant changes in meaning. “Young woman” becomes “virgin”.

  51. 51
    Origenes says:

    Allan Keith: In the real world, the frequency and speed of environmental change means that these islands fluctuate between islands, plains and valleys.

    Obviously not at the level of say ATP synthase,as GPuccio points out. End of story.

    However, I think you are correct, the environment of an organism is constantly changing in a myriad of ways. I am happy to agree with you on this, since this poses a problem that goes to the heart of Darwinism.

    The whole idea of why organisms exist in the first place, if I understand unguided evolution correctly, is that an happenstance material structure (organism) fits an environment. It is because of this tight fit that they exist at all. Why else?

    But if the environment is in a constant flux, on which we seem to agree, then the whole story breaks down. If there is not one stable environment to fit, but, instead, an environment which is constantly changing, then what can explain the continuous “fitness”?

  52. 52
    Allan Keith says:

    Origenes,

    Obviously not at the level of say ATP synthase,as GPuccio points out. End of story.

    We agree to disagree.

    The whole idea of why organisms exist in the first place,

    I think that is the major difference in our views. You keep looking for “why”, which is beyond evolution. We only deal with “how”. Some may feel that this isn’t enough, but that is the problem for people seeking the “why”.

    If there is not one stable environment to fit, but, instead, an environment which is constantly changing, then what can explain the continuous “fitness”?

    That is your problem right there. Fitness is always relative, not absolute. There is no such thing as continuous fitness. Whoever survives to reproduce is more fit than those who don’t.

  53. 53
    OLV says:

    RV+NS could easily produce this given many years to try:

    ATP Synthase: The power plant of the cell

    ATP Synthase

    ATP synthase: Structure and Function

    The Bacterial Flagellar Motor

    The factual evidences are well documented all over the scientific literature.

    We just don’t understand it.

  54. 54
    kairosfocus says:

    AK,

    It seems “fallacy” here is ,little more than a policy of rhetorical dismissal. I note on points:

    >>the whole idea of isolated islands of functional space is a fallacy.>>

    1: Argument by dismissive tag not demonstration.

    2: The metaphor obtains as FSCO/I requires that a significant number of components be properly oriented, arranged and coupled to achieve configuration-based function. (As an instance, consider glyphs arranged as alphanumerical characters to express meaning or to express a program.)

    3: As a consequence, we may contemplate vastly more configurations where parts are clumped at random, thus resulting with all but certainty in non-function.

    4: Beyond, we contemplate the even vastly more cases where parts may be scattered across a physical space. Components of a fishing reel are a simple example. So would be the components of a von Neumann kinematic self-replicator involving a universal constructor.

    5: Thus, islands of function in a configuration space are a common reality, not a fallacy.

    >> In the real world,>>

    6: You and others of similar persuasion have made no real world demonstration of blind chance and mechanical necessity giving rise to FSCO/I per actual observation.

    7: A speculative, imagined, too often ideologically loaded reconstruction of the remote unobserved actual past is being put on the table as though it were fact.

    8: where also, for years it has been on the table to contemplate islands of function that are much like sandy barrier islands and sand dunes: shape-shifting and mobile.

    9: That simply underscores that the issue is not moving around within an island but getting to the shores of the first relevant island [OoL] then onward passing seas of non-function to get to onward ones.

    10: Further, we should recall that protein fold domains are deeply isolated in AA sequence space

    >> the frequency and speed of environmental change means that these islands fluctuate between islands, plains and valleys.>>

    11: Red herring led away to strawman caricature: you have substituted for search challenge to get TO an island the task of hill-climbing within such an island.

    12: Not entirely successfully either, first the mut rate, proportion of “beneficials” and pop genetics challenge of fixing would collapse in the face of the sort of rapidity you suggest.

    13: Second, you skip over the problem that a shape-shifting domain is not a smoothly varying one on the rates you suggest, leading to undermining differential reproductive success as a filter so turning this into pure chance search. That is, you have undermined the very framework you imply appealing to.

    14: Back on main point, you have not addressed the key issue: how to cross seas of non-function to arrive at shores of an island, at OoL and at origin of body plan.

    15: Shape-shifting mobile islands in which peaks become valleys and vice versa in rapid succession then compound the problem by undermining the generalised incremental hill climbing that is sought.

    KF

    PS: I suggest you go to sites that discuss exegesis if you want to play at exegete. I suggest, though, that your assumption on renderings of alma [and parthenos in the C3 BC Septuagint] are not the last word, whatever confident manner declarations may have been fed to you. That you imagine that such a further red herring exercise would be effective speaks volumes on a day when you have exposed yourself as imagining that evil is an empty “religious” construct.

  55. 55
    kairosfocus says:

    OLV, ATP Synthase, 1st e.g. is antecedent to a functional cell of observed type, given significance of ATP. Just for starters. KF

  56. 56
    Origenes says:

    Allan Keith @

    O: The whole idea of why organisms exist in the first place, if I understand unguided evolution correctly, is that an happenstance material structure (organism) fits an environment. It is because of this tight fit that they exist at all. Why else?

    Allan Keith: I think that is the major difference in our views. You keep looking for “why”, which is beyond evolution. We only deal with “how”. Some may feel that this isn’t enough, but that is the problem for people seeking the “why”.

    What a ridiculous response!

    According to (materialistic unguided) evolution there are material structures (organisms) which exist for some reason. Right? Law, chance or whatever. And it has to do with fitting an environment.
    Or are you saying that evolutionary theory offers no explanation at all for why organisms exist and continue to exist?

  57. 57
    Allan Keith says:

    KairosFocus,

    AK,

    It seems “fallacy” here is ,little more than a policy of rhetorical dismissal.

    As opposed to “Darwinian Debating Device”? What are you up to now? 17? 18? 19?

    With regard to islands of function, if it is more like a seascape than a landscape, as you have admitted, how do you continue to claim that the “search space” is insurmountable? Ignoring for the moment that evolution is not s search. If a mutation (or other source of variation) results in increased fitnes it will be more likely to become fixed in the population.

    For example, the poster boy of IC, the flagellum, is highly variable from species to species. And there are components of the flagellum that perform non locomotive functions. How can something be irreducible complex if it is so variable in structure, and if it’s components perform other functions?

    Or are you going to declare my response a DDD and dismiss it?

  58. 58
    Allan Keith says:

    Origenes,

    According to (materialistic unguided) evolution there are material structures (organisms) which exist for some reason. Right?

    Wrong. They exist. How they exist is what science looks for. Why they exist is left up to theists.

    Or are you saying that evolutionary theory offers no explanation at all for why organisms exist and continue to exist?

    I am saying exactly that. “Why” is not a question we can answer. At best, we can answer “how”.

    I thought that everyone knew this. It is one of the fundamentals of science.

  59. 59
    kairosfocus says:

    AK, you were just answered point by point — again — on your attempt to dismiss the islands of function concept. You twisted what I said to further play at strawman games. That is telling. I suggest that you address the reason why deeply isolated islands exist by the inherent nature of configuration-based function dependent on multiple, correctly oriented, arranged and coupled parts. When you can acknowledge the reality behind fishing reels, car engines, clocks, instruments on a 747 instrument panel, the jet itself, oil refineries, text in sentences, computer programs, D/RNA, molecular machines, cellular metabolic networks, cellular machines such as ribosomes and ATP synthase, the flagellum etc, then there is common ground for serious discussion. As a part of that discussion, we can then address the claim that such islands may sometimes be like barrier islands with dunes: moving and shape-shifting in their slopes. Then, maybe you can face the implication of your rapidity of such motions claim i/l/o the issues on low beneficial mutation rates, population genetics and sizes, time to fix changes, and more. along the way, the gap between what that would imply and the cross section sample of life forms across the ages and the systematic gaps that undermine gradualistic, [neo-]darwinist accounts of body plan level [macro-]evolution will also be relevant, including WHY Gould et al proposed punctuated equilibria. Meanwhile we must not lose sight of the trillion member observation base that the only actually observed cause of the FSCO/I involved is intelligently directed configuration. Where, it is obvious that you have no answer to the challenge of blind needle in a vast haystack search so you set out to rhetorically distract from the observed pattern of islands of function in large config spaces. In the context of cell-based, protein-using life, this includes the pattern of thousands of protein fold domains that are structurally isolated in AA sequence space, including a large number of small domains such that closely neighbouring species are often deeply isolated at the critical level: molecular machinery in their constituent cells — starting from the zygote or equivalent. KF

    PS: FYI, a how answer is a rationale by mechanism and so is also a why answer. Why do planets and comets etc orbit on arcs following conic sections (with perturbations)? Because of gravitational mechanics driven by inverse square law flux based forces and resulting fields. In turn, mass warps the fabric of space-time leading to said fields. Why answered by how, reflecting the weak form principle of sufficient reason: for any entity or phenomenon or being x, we may ask why is x so and pursue an investigation. A mechanism and/or stochastic pattern giving rise to x under certain initial and circumstantial conditions is an answer at one level. Similarly, as with the text of your own comments, intelligently directed configuration affecting stochastic-dynamic patterns may be a further level of relevant causal factor. And more.

    PPS: It should be increasingly evident that there are systematic gaps, misunderstandings, distortions and outright cases of incoherence in your arguments as seen here at UD recently. This points to another pattern, that you are following a broken worldview or movements that try to accommodate to it. Evolutionary materialist scientism is utterly and irretrievably self-referentially incoherent and self-falsifying. It should be set aside and attempts to fit in with it should be abandoned.

  60. 60
    gpuccio says:

    Allan Keith at #47

    “I have no idea.”

    I appreciate your second “no”.

    “I was just criticizing the nonsense of the isolated island of function that evolution must cross. Because of environmental change, geographic isolation, etc. This concept has long been discredited. The fitness landscape is more like a stormy sea. What was insurmountable yesterday is a flat plain today and a down hill run tomorrow. Lame metaphors, I know, but no more lame than the whole “islands of function” metaphor.”

    There is no nonsense at all in the idea of isolated islands. As you can see in the example of my OP, they are absolute realities.

    We have 2000 protein superfamilies, which are isolated islands by definition: isolated at the level os sequence, structure and function. What more do you want?

    The idea that envirnmental changes can help reach isolated islands of function os completely silly. The environment, of course, has no idea of how an ATP synthase can be built, least of all of what sequence the alpha and beta chain must have so that the F1 structure can work. Indeed, the environment has no idea at all that ATP exists, and of what it can be used for.

    It’s like saying that chabges in the number of students, or in the TV programs they look at, can help generate paragraph P by mere RV and NS. That’s not true, of course. The only way you can generate paragraph P is if you know what you want to say, and say it (design it).

    The “fitness landscape” is, at most, a potential request: like saying that the market is ready for a new kind of car. But someone must design the new car, it will not come into existence only because the environment can receive it.

  61. 61
    gpuccio says:

    goodusername at #48:

    Considering that if you take any two random novels and compare them that they’ll almost certainly be essentially 0% alike, I don’t think that’s a good analogy to what we find with lifeforms.

    A closer analogy would be if you limited the comparison to, say, the various thousands of different editions of the Latin Vulgate to life. As I understand it, many editions of the Vulgate can be classed into various “families”, and there are even times where one can construct a “tree” of sorts, where you have edition “B” coming from edition “A”, and editions “C” and “D” both forking from B, etc., etc.

    No, that’s wrong.

    Take, for example, protein superfamilies. We have 2000 of them. And each one is completely unrtelated to the others, at sequence level, structure level and function level.

    So, they are not “different editions of the Latin Vulgate”. They are completely different books.

    The different proteins inside one protein family could be, maybe, compared to different editions of a same book. Or, rather, to different books on a similar subject.

    But protein suprfamilies are completely different.

    The same could be said for regulation systems. For example, the Ubiquitin system is a book of its own. It is different from other regulation systems, like DNA methylation, or Histone methylation, or miRNAs, and so on. Different books, all of them.

  62. 62
    gpuccio says:

    Allan Keith at #50:

    “Actually, a better analogy might be the evolution, and variation, of Christian scriptures over the last 2000 years. Subtle changes, yet significant changes in meaning. “Young woman” becomes “virgin”.”

    Please, see my answer to goodusername at #61.

  63. 63
    kairosfocus says:

    PPPS: I add: Where different fishing reels have differing parts that work in somewhat different ways and cannot typically be substituted, where also, in a market, reel technology evolves so the successful products shape and configuration shift while still conforming to the deeply isolated islands of function pattern. At a given time many diverse reels are viable, each in a niche. It should surprise no one that there are many models of flagellum that work each in its own FSCO/I rich way . . . and notice, this goes beyond irreducible complexity claims. If you imagine that blind exaptation explains away irreducible complexity and wider FSCO/I, I suggest you explain to us the phenomenon of auto parts stores and the like and why similar parts don’t typically work in diverse car engines etc. Yes, auto parts stores are relevant evidence, as are electronics and electrical or industrial part catalogues.

  64. 64
    gpuccio says:

    Allan Keith at #52:

    “I think that is the major difference in our views. You keep looking for “why”, which is beyond evolution. We only deal with “how”. Some may feel that this isn’t enough, but that is the problem for people seeking the “why”.”

    As for me, I would be perfectly satisfied by the “how”. So I ask:

    How?

  65. 65
    kairosfocus says:

    GP, good summaries, thanks for using the same proteins in AA sequence space (and wider org chem space) example. KF

  66. 66
    kairosfocus says:

    GP, I note that the two sorts of answers are related once one sees the significance of a weak form PSR. Let me clip:

    a how answer is a rationale by mechanism and so is also a why answer. Why do planets and comets etc orbit on arcs following conic sections (with perturbations)? Because of gravitational mechanics driven by inverse square law flux based forces and resulting fields. In turn, mass warps the fabric of space-time leading to said fields. Why answered by how, reflecting the weak form principle of sufficient reason [wf-PSR]: for any entity or phenomenon or being x, we may ask why is x so and pursue an investigation. A mechanism and/or stochastic pattern giving rise to x under certain initial and circumstantial conditions is an answer at one level. Similarly, as with the text of your own comments, intelligently directed configuration affecting stochastic-dynamic patterns may be a further level of relevant causal factor. And more.

    That is, we exhibit confidence in the coherence and substantial intelligibility of our world, which are foundational to the long-term health of science, technology and civilisation.
    KF

  67. 67
    gpuccio says:

    Allan Keith at #57:

    “If a mutation (or other source of variation) results in increased fitnes it will be more likely to become fixed in the population.”

    True, but those mutations will not lead to new, roiginal and complex information. Like typo corrections will not lead to paragraph P.

    I think the idea is clear enough. It’s not that the ocean cannot be traverses, the point is that even if you traverse it you have no reasonable probability of finding the islands, because the islands are too small, and the ocean is too big.

  68. 68
    gpuccio says:

    KF at #59:

    “PS: FYI, a how answer is a rationale by mechanism and so is also a why answer.”

    Thank you for clarifying that! 🙂

    It should be obvious, but it seems that it’s not.

    I hope that now AK will give us the “how”! 🙂

  69. 69
    kairosfocus says:

    GP, there has been a skeptical challenge to the concept of cause and a similar one to confidence in the substantial intelligibility of phenomena. Those who promote such don’t seem to be aware of just how damaging that is to the roots of science. Just the other day, I had a conversation with someone who tried to dismiss macroeconomics because of seeing similarly qualified profs propose seemingly opposed solutions to the economic stagnation problem. I drew a diagram of As-Ad, with aggregate supply saturating at some level of national income due to input bottlenecks so that pushing aggregate demand beyond leads to inflation rather than growth. The difference between deep recession and stagnation because of running out of room for growth (often, due to shocks like the volcano disaster here or oil price or financial disasters) was then brushed aside. The point is, we are undermining the basis for progress when we undermine confidence in the substantial intelligibility of our world. Of course, the confidence in the power of mind, reasoning, logic, induction etc is deeply akin to confidence that our world is rationally structured, a cosmos not a chaos. That in turn points to how our minds are governed morally by duties to truth, care and correctness in reasoning, justice etc, thence the need for IS and OUGHT to be bridged at world root level. That in turn is a compass needle pointing to the only serious candidate after centuries of debate: the inherently good and wise creator God, a necessary and maximally great being worthy of the responsible, reasonable service of doing the good in accord with our evident nature. The very shadow of God is utterly frightening and repugnant to too many and in their haste to flee, they do serious harm to the roots of sound progress. KF

  70. 70
    gpuccio says:

    KF at #69:

    🙂 🙂 🙂

  71. 71
    Origenes says:

    Allan Keith @52 @58

    Okay then …. Let me rephrase my question:

    According to unguided evolution, HOW do (material structures) organisms exist, and continue to exist, in an environment?

    Correct me if I am wrong, but ‘by fitting the environment’, is the only answer that I am aware of. The idea seems to be that as long as the organism fits the environment it does not fall apart.

    Back to my point in #51:
    So we have two distinct material systems: the environment and the organism. And the two “fit.”

    Now, if the environment is in a constant flux, the organism has to keep up with those changes in order to maintain the “fit”. But, again, and this is my point, there is no materialistic explanation for how this “synchronicity” can be maintained.

  72. 72
    kairosfocus says:

    Origenes, let’s go to a time and place on the conventional timeline: Yucatan or thereabouts, 65 MYA, cosmic impact. Suddenly, dinosaur era is catastrophically devastated and scurrying mammals underfoot get their chance to shine. Has the space of functional protein families in AA sequence space materially shifted? No, chemistry has not changed and protein clusters still do their jobs. Has body-plan level functionality shifted? Ecosystems have collapsed, mass extinctions happen due to loss of habitat and logistical support for life forms. Suppose much the same happened today, would the human genome fail? No, though population and civilisation would collapse and there may be nowhere to go. So, we see that islands of function at grand anatomy and lifestyle matched to environment level can change catastrophically, leading to mass subtractions from the reproductive chain. Maybe, the devastated terrain and seas have room that other creatures may now move in, much as happened with overfishing or pollution [I think here of Hudson river Tomcods] and invasive species, or else maybe something like sickle cell trait confers ability top survive long enough to have a few children. Has such suddenly created novel FSCO/I or formed a mechanism capable of creating such? No, this question is unanswered; we are just seeing talking points designed to polarise against hearing a case and taking it seriously. It remains, therefore, that the only empirically observed, analytically plausible source for FSCO/I is still intelligently directed configuration. The AK challenge fails, never mind that it is doubtless being touted in the usual places in the penumbra of ideologically motivated and too often utterly uncivil objection sites. Which sites have yet to soundly put up actual observation of FSCO/I originating by blind chance and/or mechanical necessity. KF

  73. 73
    gpuccio says:

    Allan Keith:

    The point is simple, after all.

    You can’t find the islands because they are too small, and the ocean is too big.

    Changes in the environment are not a storm in the ocean: they can only point to what islands should be selectable, but if no island has been found, none is selectable any way.

    The “navigation” in the ocean of sequences is due to RV. RV has a definite rate. It can generate a slow walk (single mutations) or some quick jerk (like in the case of frameshift mutations), but however the number of tested states is what it is.

    So, your metaphor of storms in the ocean is simply wrong. And even if it were right, a storm cannot help you find islands that are too small to be found: your boat will be tossed in the ocean anyway, without finding land.

  74. 74
    ET says:

    Allan:

    As ID has no idea how it was designed and incorporated into living organisms.

    ID knows that it was intelligently designed and incorporated into living organisms.

    On the other hand your position is all about the how and yet no one has any idea how blind and mindless processes could have produced ATP synthase.

    But the whole idea of isolated islands of functional space is a fallacy.

    Cuz you say so? Really?

    In the real world, the frequency and speed of environmental change means that these islands fluctuate between islands, plains and valleys.

    Pure gibberish. ATP synthase remains isolated regardless of the environment. All bacterial flagella remain isolated regardless of the environment. All irreducibly complex structures and systems remain isolated regardless of the environment.

    Allan Keith is just spewing nonsense.

  75. 75
    ET says:

    Allan:

    For example, the poster boy of IC, the flagellum, is highly variable from species to species

    Your position has nothing to account for any of them

    And there are components of the flagellum that perform non locomotive functions.

    And your position doesn’t have a mechanism that can produce them, either.

    How can something be irreducible complex if it is so variable in structure, and if it’s components perform other functions?

    That doesn’t affect IC at all. If you think that it does then it is up to you to make your case. If you can’t then you know why it doesn’t affect IC at all.

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

  76. 76
    LocalMinimum says:

    Attempting to rephrase a portion of what KF said @ 54, environment only determines selection parameters, and selection can only select functionality that could work towards reproductive success.

    Most possible combinations of letters are gibberish; most possible combinations of computer program instructions are compile time errors, run-time errors, or fail to yield non-error output; and most genetic arrangements are dead.

    Can’t select what fails to work towards reproductive success in any context, and there’s no “Mickey” environment to make a champion out of a stillborn proto-critter via a Rocky-style training montage.

  77. 77
    Mung says:

    Every possible sequence and every possible combination of letters has a function, we just haven’t discovered it yet.

    I propose that the function of such sequences is to show how rare function really is.

    ?Therefore, all sequences are functional.

    Q.E.D

  78. 78
    Allan Keith says:

    Origenes,

    Now, if the environment is in a constant flux, the organism has to keep up with those changes in order to maintain the “fit”. But, again, and this is my point, there is no materialistic explanation for how this “synchronicity” can be maintained.

    In many cases, it is not maintained. The fossil record is full of organisms that did not survive.

  79. 79
    LocalMinimum says:

    AK @ 57:

    For example, the poster boy of IC, the flagellum, is highly variable from species to species. And there are components of the flagellum that perform non locomotive functions. How can something be irreducible complex if it is so variable in structure, and if it’s components perform other functions?

    Reusable components are a good practice in software engineering. Interestingly, while I constantly see reuse in functions, I don’t expect to see a non-IC function, i.e. a function that performs some function, then performs it better and better with a simple addition of parts and no modification of the rest of the function to accept those parts.

    Even if I should find a function that is nothing but function calls to functions that aren’t subfunctions for organization’s sake, but are generally useful, with no other code, the parameter arrangements in each call are still specific to that greater function. This would be analogous to the necessary configuration data in the hypothetical “biological system comprised of fully-reusable- in-other-contexts components” case you’re probably reaching for.

    Reusable structure can be trivially contained within IC structures. Variation means nothing of itself if it doesn’t offer a continuity between variants and a precursor that could’ve come from “elsewhere”. Variation between flagellum could just be marking the highest points on a handy functional island.

    If there’s a leap to be made, there’s a leap to be made. And if there’s a leap that can’t be made…

  80. 80
    gpuccio says:

    LocalMinimum at #79:

    Very good points! 🙂

  81. 81
    kairosfocus says:

    F/N: on the exaptation talking point — which should have long since been put out to pasture as unworkable, Menuge:

    IC is a barrier to the usual suggested counter-argument, co-option or exaptation based on a conveniently available cluster of existing or duplicated parts. For instance, Angus Menuge has noted that:

    For a working [bacterial] flagellum to be built by exaptation, the five following conditions would all have to be met:

    C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.

    C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.

    C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.

    C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.

    C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.

    ( Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)

    In short, the co-ordinated and functional organisation of a complex system is itself a factor that needs credible explanation.

    However, as Luskin notes for the iconic flagellum, “Those who purport to explain flagellar evolution almost always only address C1 and ignore C2-C5.” [ENV.]

    KF

  82. 82
    gpuccio says:

    LocalMinimum at #79 and KF at #81:

    Excellent thoughts! 🙂

    As I debated a long time ago, one of the recurring fallacies of neo-darwinists is to minimize and underemphasizing function and complexity.

    We should, after all, have compassion for them: they desperately need a biological world that is as simple as possible, and have to live in the real world, where every single day new papers and new research ouline the ever increasing complexity of what we know, and the infinely increasing glimpsed complexity of what we still don’t know.

    So, they like to thing that functional modules work like Lego bricks: simple units that even a child can recombine easily, getting new and original scenarios of function. So, exons and domains and maybe even secondary structures become imaginary construction elements, ready to be shuffled, recombined, thrown like dies to win some very unlikely prize.

    But that is not the case: whoever has tried object oriented programming, or even modular engineering, knows all too well that modularity worls only in a refined design context, in a very intelligent adjustment where different plans and different ideas are made to cooperate in harmony. Modularity is the triumph of design, not its negation.

    And, after all, even a child working with Lego bricks is a much greater engineer than blind chance, which would not even be able to connect them effectively.

  83. 83
    harry says:

    gpuccio @82,

    … they desperately need a biological world that is as simple as possible, and have to live in the real world, where every single day new papers and new research ouline the ever increasing complexity of what we know, and the infinely increasing glimpsed complexity of what we still don’t know.

    I have been reading up on protein synthesis. There is a lot of info on the web that goes into great detail, from DNA nucleotides, to codons to mRNA and tRNAs, tRNA synthetase, ribosomes, etc.

    It is all quite amazing. Having worked with low-level technology most of my adult life, software more than hardware, but hardware too, I know technology when I see it. The more I read about protein synthesis, the more painfully obvious it is to me that this is technology, which is by definition the application of scientific knowledge for a purpose.

    I think biologists ought to be required to program a digital telephony switch, or write software that simulates the instruction set of a CPU, or write communication software to manage robotic equipment on the factory floor, so they would recognize technology when they see it.

  84. 84
    gpuccio says:

    harry:

    Yes, it is technology, and great technology, I would say.

    And getting this level of control with biological molecules is much more difficult than working with tranistors or conventional machines. The laws that govern the biological world, indeed, are much more difficult to understand and harness.

    It’s not a case that we are still trying to understand, and the more we understand, the more we discover new levels of complexity and control. It’s really amazing.

  85. 85
    gpuccio says:

    To all:

    This comes from my monitoring of new papers about the ubiquitin system. It is brand new (May 9), and I cross-post it from the Ubiquitin thread, because it is a very good example of the things we have just discussed here:

    The E3 ubiquitin ligase UBR5 regulates centriolar satellite stability and primary cilia.

    https://www.ncbi.nlm.nih.gov/pubmed/29742019

    Abstract:

    Primary cilia are crucial for signal transduction in a variety of pathways, including Hedgehog and Wnt. Disruption of primary cilia formation (ciliogenesis) is linked to numerous developmental disorders (known as ciliopathies) and diseases, including cancer. The Ubiquitin-Proteasome System (UPS) component UBR5 was previously identified as a putative positive regulator of ciliogenesis in a functional genomics screen. UBR5 is an E3 Ubiquitin ligase that is frequently deregulated in tumours, but its biological role in cancer is largely uncharacterised, partly due to a lack of understanding of interacting proteins and pathways. We validated the effect of UBR5 depletion on primary cilia formation using a robust model of ciliogenesis, and identified CSPP1, a centrosomal and ciliary protein required for cilia formation, as a UBR5-interacting protein. We show that UBR5 ubiquitylates CSPP1, and that UBR5 is required for cytoplasmic organization of CSPP1-comprising centriolar satellites in centrosomal periphery, suggesting that UBR5 mediated ubiquitylation of CSPP1 or associated centriolar satellite constituents is one underlying requirement for cilia expression. Hence, we have established a key role for UBR5 in ciliogenesis that may have important implications in understanding cancer pathophysiology.

    Now, UBR5 is an E3 ligase of exceptional length: 2799 AAs. This is the “function” section at Uniprot:

    “E3 ubiquitin-protein ligase which is a component of the N-end rule pathway. Recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation (By similarity). Involved in maturation and/or transcriptional regulation of mRNA by activating CDK9 by polyubiquitination. May play a role in control of cell cycle progression. May have tumor suppressor function. Regulates DNA topoisomerase II binding protein (TopBP1) in the DNA damage response. Plays an essential role in extraembryonic development. Ubiquitinates acetylated PCK1. Also acts as a regulator of DNA damage response by acting as a suppressor of RNF168, an E3 ubiquitin-protein ligase that promotes accumulation of ‘Lys-63’-linked histone H2A and H2AX at DNA damage sites, thereby acting as a guard against excessive spreading of ubiquitinated chromatin at damaged chromosomes.”

    Now, this protein has an amazing jump in human-conserved information from pre-vertebrates to vertebrates:

    2098 bits (0.75 baa)

    The human protein and the protein in cartilaginous fish (callorhincus milii) show the following homology:

    4913 bits
    2574 identities (92%)
    2690 positives (95%)

    IOWs, this very long protein has remained almost the same for 400+ million years!

    Uniprot recognizes only two domains in the C terminal part:

    PABC (78 AAs)
    HECT (338 AAs)

    The Blast page recognizes the same two domains, plus one small putative zinc finger (67 AA) in the middle of the sequence, and an even smaller CUE domain (64 AAs) in the N terminal part.

    IOWs, more than 2200 AAs that make up the protein, and that are extremely conserved, do not correspond to known domains.

    This is certainly an amazing example of a highly specific and very long sequence, whose complex regulatory functions we can only barely imagine, and that exhibits almost 5000 bits of functional information (conserved from cartilaginous fish to humans) more than 2000 of them appearing for the first time in the transition to vertebrates.

  86. 86
    gpuccio says:

    To all:

    Some more information about the functional relevance of UBR5. From the ExAC site (a database of human polymorphisms):

    UBR5:

    z score for the reduction in observed variants vs expected variants:

    z = 6.53

    Probability of Loss of Function intolerance:

    pLI = 1.00

    IOWs, this is an extremely functional protein, that badly tolerates variants.

  87. 87
    Origenes says:

    Allan Keith @78

    O: Now, if the environment is in a constant flux, the organism has to keep up with those changes in order to maintain the “fit”. But, again, and this is my point, there is no materialistic explanation for how this “synchronicity” can be maintained.

    Allan Keith: In many cases, it is not maintained. The fossil record is full of organisms that did not survive.

    Sure, but death is not in need of an explanation; life is. The first is in perfect accord with materialism, the second is not.

    As you rightly point out, in # 43, the environment of an organism is in a constant flux and ever-changing. A myriad of factors — e.g. sun, clouds, temperature, water, soil, plants, animals — guarantee that the environment is never the same. So, contrary to what Darwin envisioned, there is no such thing as one stable environment and eons of time to adjust to it.

    Indeed, an organism is not a fixed material structure, which “fits” one fixed stable environment. Even a single cell can be said to be never the same during its life cycle.

    So, we have two distinct material systems: the environment and the organism. And the two continually “fit.” My claim is that there is no material explanation for this continuous fit — the synchronicity between environment and organism.

    Given materialism, there is no organism that wants to fit an environment. There is just chemistry, which does not care less whether it fits the environment or not. So there is no reason why two distinct material systems — the environment and the organism — act in synchronicity.

  88. 88
    gpuccio says:

    Allan Keith and Origenes:

    I would like to emphasize a point which is often overlooked.

    A lot is said about the environment, and about how its changes can shape living organisms. That’s probly because the best examples where we can imagine NS acting are drmatic changes in the environment. So, mass extinctions are often explained that way. And competition between species is also considered a major factor.

    Now, I don’t want to deny or underemphasize the role of environment changes in shaping many important events in natural history. But we often forget that many basic functions of life, indeed most of them, are not directly linked to environment, if not in the very general sense of engineering life in a certain basic environment on our planet.

    Of coruse, the way our planet is, and its different scenarios, are the basic context for life. But that basic context does not change so rapidly, after all. The basic resources, sunshine, oxygen, and so on, are rather constantly present, at least after the first major adaptations of the planet. Photosynthesis works today as it worked a lot of time ago. The basic metabolisms, or the basic systems to duplicate, transcribe and translate DNA have remained the same for a very long time.

    What I mean is: life develops, in many ways, in the presence of important constraints from the environment, which can certainly change, but also in the presence of important constraints coming from the mechanisms themselves of what life is, and of what life is trying to express.

    For example, IMO it is really difficult to explain teh appearance of eukryotes as an adaptation to environment. Prokaryotes have alwys been the most successful beings on our planet in terms of reproduction, flexibility, resistance to extreme contexts. There is nothing lacking in them.

    So, why and how could the huge added complexity in the eukaryotic celll originate?

    The only reasonable answer is: the eukaryotic cell is much more complex, and therefore it has greater potentialities to express higher functions. Including the development of multicellular organisms.

    Much of the huge informational novelty that we find in eukaryotes is not an adaptation to some change in the environment, but rather a necessary jump in engineering concepts. It’s like passing from the cart to the petrol engine car, not because the environment has changed, and made carts no more functional, but because we want to express new and more powerful functions.

    But of course, it’s no that the petrol engine car can originated from random changes to the cart, and then suddenly be selected for its greater speed. It’s a new, original idea. A jump in engineering, a new concept, and it requires the harnessing of a lot of specific functional information to be implemented, even at a minimal level.

    How could a change in environment cause the ubiquitin system? Or the spliceosome? What does the environment know of ATP synthesis, or of immunity?

    Adaptation to environments is a real and important factor, but it has been certainly oversold.

  89. 89
    Origenes says:

    kairosfocus @72

    KF: Yucatan or thereabouts, 65 MYA, cosmic impact. Suddenly, dinosaur era is catastrophically devastated and scurrying mammals underfoot get their chance to shine. Has the space of functional protein families in AA sequence space materially shifted? No, chemistry has not changed and protein clusters still do their jobs.

    I agree. Allan Keith’s argument about environmental fluctuations does not apply to this level. And it is this level that is addressed by GPuccio’s OP. So, Keith’s argument fails.

    KF: Has body-plan level functionality shifted? Ecosystems have collapsed, mass extinctions happen due to loss of habitat and logistical support for life forms. Suppose much the same happened today, would the human genome fail? No, though population and civilisation would collapse and there may be nowhere to go. So, we see that islands of function at grand anatomy and lifestyle matched to environment level can change catastrophically, leading to mass subtractions from the reproductive chain.

    Given materialism and unguided evolution, such a dramatic change of the environment should lead to total extinction. The organisms are simply not adapted to the new environment.

    But the point I try to put forward is that even every day changes in the environment, should also be expected to demolish the fitness of ANY organism. If it is all blind chemistry, why does the whole thing not fall apart?

    I argue that there is no such thing as a single fixed stable environment to adapt to. “The environment” is not one thing but, instead, a collection of countless states — ever alternating in succession. The problem for evolutionary theory is not to explain adaptation to ‘one stable environment’, but, instead, adaptation to ‘countless environments’ and countless alternations between them.

  90. 90
    harry says:

    gpuccio @88,

    Prokaryotes have always been the most successful beings on our planet in terms of reproduction, flexibility, resistance to extreme contexts. There is nothing lacking in them.

    So, why and how could the huge added complexity in the eukaryotic cell originate? …

    The only reasonable answer is: the eukaryotic cell is much more complex, and therefore it has greater potentialities to express higher functions. Including the development of multicellular organisms.Much of the huge informational novelty that we find in eukaryotes is not an adaptation to some change in the environment, but rather a necessary jump in engineering concepts. It’s like passing from the cart to the petrol engine car, not because the environment has changed, and made carts no more functional, but because we want to express new and more powerful functions.

    Excellent point!

    An environment conducive to life arising was just as unlikely to be arrived at mindlessly and accidentally as it was for the massive functional complexity of the self-replicating, digital-information-based nanotechnology of life to be arrived at that way.

    There are individuals who, because they are extremely naive about what it takes to develop software, could be convinced that a given suite of functionally complex applications running on a computer actually came about mindlessly and accidentally. But there are very, very few individuals who would believe, in addition to that, that the computer itself came about mindlessly and accidentally. Yet that is basically what contemporary atheism is asking the world to believe.

    Life is a suite of complex applications running in an environment that was far more unlikely to be arrived at mindlessly and accidentally than were the computer and operating system required by any functionally complex software.

    Just how unlikely was it that the Big Bang would produce an environment where life was a possibility? Roger Penrose, in his book The Road to Reality: A Complete Guide to the Laws of the Universe, calculates that the odds of the Big Bang mindlessly and accidentally producing a universe where life would be a possibility were one in 10^10^123.

    The double exponent makes that number so large that one can have far more certainty that the universe was not a mindless accident than one can have that the laws of physics will continue to apply consistently to nature.

    So unless, I suppose, one has all their possessions tied down just in case gravity stops working, it should now be apparent that it is simply irrational to conclude that the Universe and the living things within it are mindless accidents.

    Let’s be honest: The survival of the macro-evolution claims of Darwinism are due to their affinity with militant, intrinsically faith-based atheism, not due to rational, objective analysis of the available evidence.

  91. 91
    Mung says:

    gpuccio:

    So, they like to thing that functional modules work like Lego bricks: simple units that even a child can recombine easily, getting new and original scenarios of function.

    LEGO pieces are so poorly designed. No intelligent designer would have created them.

  92. 92
    Allan Keith says:

    Just a clarification on my comment about changing environment. This is not limited to climate and other physical changes. It also includes things like population density changes, increased predation, etc.

  93. 93
    gpuccio says:

    Allan Keith at #92:

    Yes, I understand that.

    But the point remains: environment can differentially select he various solutions present in the pool of organims: favour some vs others.

    But it cannot build the solutions. The solutions are complex functions, and environment has no information about how to solve problems. It can only select the solution that works more than the others.

  94. 94
    Allan Keith says:

    gpuccio,

    But the point remains: environment can differentially select he various solutions present in the pool of organims: favour some vs others.

    But it cannot build the solutions. The solutions are complex functions, and environment has no information about how to solve problems. It can only select the solution that works more than the others.

    It may not build the solutions but it certainly causes the direction of these changes to be limited. Obviously this can be a negative in some cases. But it can also be a positive.

  95. 95
    LocalMinimum says:

    AK @ 92:

    To be consistent, I would refer to “environment” as every available selective parameter, endogenous or exogenous to the population, biome, habitat, etc.

    The dirty little secret about “environment” and “selection” is that they’re constraints, i.e. they reduce the set of immediately viable functional configurations. They make more things fail to reproduce/less things able to thrive.

    Adding more selective pressures makes your islands smaller. That’s how selection works.

  96. 96
    gpuccio says:

    Allan Keith:

    Nobody is denying that selection exists, and that it contributes to the direction of natural history.

    It’s the same as saying that the conditions and quality of streets is a factor in the car market.

    Selection can select between those complex functions that already exist.

    Selection can select simple variant that can realistically arise from RV, if they have any effect on fitness.

    But again, the point is: how can selection build complex function? How can it find the 2500+ specific AAs that contribute to the function of UBR5? (see comments #85 and 86).

    Complex function are not the sum of simple variants, no more than paragraph P can arise from typos.

  97. 97
    gpuccio says:

    LocalMinimum at #95:

    Very good points. Constraints cannot guide engineering. They can only inspire it.

    But engineering is born in the consciousness of the engineer, who is often aware of the constraints that he has to meet.

  98. 98
    LocalMinimum says:

    Ahhh, yes, one caveat: Constraints endogenous to the population can be removed/traded by selecting against the members of the population that they emerge from. Thus, “more things could possibly thrive….with respect to population endogenous constraint.”

    However, it doesn’t affect the island shrinking effects of population exogenous selective pressure. Also, as Gpuccio’s argument is made irrespective to population endogenous constraint, however much you reduce it, the islands still become smaller with its introduction.

  99. 99
    Origenes says:

    LocalMinimum @95

    Excellent point. “Natural elimination” would be a more appropriate term.
    In the words of the madman himself:

    Charles Darwin:

    Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows.

  100. 100
    gpuccio says:

    To all:

    At the cost of seeming repetitive, I would like to insist that the crucial point in all this discussion is the origin of complex functional information.

    For its same nature, complex functional information cannot arise from blind processes where no specific information about it is present.

    So, either that information is already there in some form and is recycled, or it is generated by conscious processes of understanding and purpose.

    That is very important: conscious processes are not blind: they are the only known processes that create new functional information easily, in huge quantities. There is an intuitive quality in intelligent representations that makes it possible to harness contingency to a purpose, through intuitive understanding of meanings.

    The environment can give feedbacks about the existing solutions: that’s the same kind of feedback that an engineer can receive from outer sources, in the course of the engineering process.

    But the environment does not know how to build the solutions. That information is not in it.

    For example, the environment certainly includes the working of biochemical laws, but it does not include the understanding of those laws.

    So, while the environment can certainly tell if a protein folds or not, once the protein exists and is in the right setting, the environment cannot tell anyone which sequences will fold or not fold, unless each of those sequences is brought into existence and tested.

    But conscious processes are different: in conscious intelligent processes we can try to understand the laws by which proteins fold. Understanding the laws is completely different from just witnessing their workings. Understanding is a conscious process, it requires conscious representations and intuitions. The environment can help us to understand, providing data, but the environment cannot make us understand. Only our consciousness understands.

    And that makes all the difference. Once we understand the laws, we can apply them. In time, we will be able to design proteins top down (it’s not easy, of course, but it is possible). In the meantime, we can already get some results by guided bottom up procedures, through our still more limited understanding.

    But blind systens can do nothing like that. To them, complex functional information is denied, unless that information is already in the system and can be recycled.

  101. 101
    gpuccio says:

    Origenes at #99:

    Yes, that “directly follows” seems rather optimistic! 🙂

  102. 102
    Origenes says:

    GPuccio: … while the environment can certainly tell if a protein folds or not, once the protein exists and is in the right setting, the environment cannot tell anyone which sequences will fold or not fold, unless each of those sequences is brought into existence and tested.

    So, it’s up to random variation (RV) to produce those sequences. However, RV cannot do it:

    The Limits of Random Mutation:
    The highest probabilistic resources are found in bacteria, due to the huge population size and high reproduction rate.
    These probabilistic resources, with a hugely optimistic estimate, are still under 140 bits.
    This means that any sequence with 160 bits of functional information is, by far, beyond any reasonable probability of being the result of RV in the system of all bacteria in 4 billion years of natural history, even with the most optimistic assumptions.
    About 2000 human proteins (10% of all human proteins) each have an information jump from pre-vertebrates to vertebrates of at least (about) 500 bits.
    source.

    It follows that the search space that RV in bacteria can cover in 4 billion years is 2^140.

    gpuccio: E3 ubiquitin-protein ligase … has an amazing jump in human-conserved information from pre-vertebrates to vertebrates: 2098 bits ..

    The search space for RV to find this protein is 2^2098.
    The search space covered by RV in bacteria in 4 billion years falls short by the impressive factor of
    2^2098/2^140 = 2^1958 =

    261054696073700716677384025655938326968297974892
    424281387694176561527970396211984247352003493803356359068394
    485572631031902146551343106541804884581362478726394169800972
    377470317698633035070190252165336892320479466392533740068730
    285082249397511228275950327307687444769746763608067393105669
    762381289661636131641373387957306717003983714693990939169759
    204788599624218265093601353346758142564094126255175336169938
    862886779422801236838504433216833566010656999046437003745620
    490425584812417491962053683506798632562153178982988557319882
    64649784129895869178627123159329932787118842218391811332767744

  103. 103
    gpuccio says:

    Origenes:

    Thank you for the very good summary.

    And that is not even the total functional information for the protein, which is almost 5000 bits: it is only the specific functional information added at the relatively short transition to vertebrates! 🙂

    By the way, how could you get the detailed result for 2^1958? I have problems with those big numbers, both in Excel and in R.

  104. 104
    Origenes says:

    GPuccio @103

    GP: And that is not even the total functional information for the protein, which is almost 5000 bits: it is only the specific functional information added at the relatively short transition to vertebrates! 🙂

    You are correct of course. The problem is, in fact, way way worse for Darwinism. Allow me to correct my mistake:

    Okay ….. a protein of 4913 bits. The search space for RV to find this protein is 2^4913.

    The search space covered by RV in bacteria in 4 billion years falls short by the mind blowing factor of (2^4913) / (2^140) = 2^4773 =

    654891425406845844729120240746503467874846511118430847973449664452593619730
    146830818059253941710054084925413062835073544221162973083267966695295652913
    730372883781099143587321140518741396653264706662978780721422765640563046919
    173453298131219553432564370305459101257035784842307422010160268635044291405
    721126492239636644765340360369427725690149368754207578839674964142316690841
    830964407339358086345963289016145207366307094730194560624060759461930734285
    913797006544241210984837599866973428841018350275304583757036732538766416404
    276172903248712395385586724865393751118319741095117823800970598558752261797
    928568056391441231198561000805116075500745298603971641395823266001551774451
    099262419131272320722715983427224181919628162912931749982978985471473424302
    462014816770413780470220937042948927060987067171909846990482964712523313090
    153100404362496007560196917462833908098360182393345547427029588869285790243
    755695905909744859003974689425451143008791436164846954918881171772936033521
    613433702449971073523736239555003554667367225319443472669380502520209016199
    960990872675119216271490809862682290518341617278786796310960836424355683256
    303546051088046731247994188059694887775912059511017425697331883773223509391
    923974066217065727885865689654519857557404943430124381212424723888586350209
    503137202030133058537587753050288132028009865386934597210207262716765286114
    436574220465408067797278115529596606091012570034841103262933667152101611118
    678499131392

    GP: By the way, how could you get the detailed result for 2^1958?

    I found this website: https://defuse.ca/big-number-calculator.htm

  105. 105
    gpuccio says:

    Origenes:

    That seems very useful, thank you! 🙂

  106. 106
    kairosfocus says:

    Origenes,

    excellent.

    2^500 =

    3 273 390 607 896 141 870 013 189 696 827 599 152 216 642 046 043 064 789 483 291 368 096 133 796 404 674 554 883 270 092 325 904 157 150 886 684 127 560 071 009 217 256 545 885 393 053 328 527 589 376

    2^1000 =

    10 715 086 071 862 673 209 484 250 490 600 018 105 614 048 117 055 336 074 437 503 883 703 510 511 249 361 224 931 983 788 156 958 581 275 946 729 175 531 468 251 871 452 856 923 140 435 984 577 574 698 574 803 934 567 774 824 230 985 421 074 605 062 371 141 877 954 182 153 046 474 983 581 941 267 398 767 559 165 543 946 077 062 914 571 196 477 686 542 167 660 429 831 652 624 386 837 205 668 069 376

    That will help those who have problems with rounded values, such as 3.27*10^150 and 1.07*10^301. Though, the rounded values give the order of magnitude with a lot more clarity.

    While I am at it, let’s look at the doubling effect of doing 2^1001:

    2^1001 =

    21 430 172 143 725 346 418 968 500 981 200 036 211 228 096 234 110 672 148 875 007 767 407 021 022 498 722 449 863 967 576 313 917 162 551 893 458 351 062 936 503 742 905 713 846 280 871 969 155 149 397 149 607 869 135 549 648 461 970 842 149 210 124 742 283 755 908 364 306 092 949 967 163 882 534 797 535 118 331 087 892 154 125 829 142 392 955 373 084 335 320 859 663 305 248 773 674 411 336 138 752

    That is, 2.14 * 10^301, pretty nearly.

    KF

  107. 107
  108. 108
    gpuccio says:

    To all:

    Maybe some of those who read my comments, when they see the examples of proteins that exhibit extreme conservation, like UBR5 and many others I have described, may think that that is a common feature.

    It is not. Most proteins have lower conservations.

    So, I will give an example just to show how different can be the behaviour of complex proteins.

    We already know of UBR5. It is an E3 ligase with important regulatory functions. As we have seen (see comment ]85).

    To recapitulate, here are the values of the blast between the human protein and cartilaginous fish:

    Length: 2799 AAs
    Bitscore: 4913 bits
    Identities: 2574 (92%)
    Positives 2690 (95%)
    baa: 1.755
    E-value: 0

    For comparison, here is another long protein with regulatory functions:

    MHC class II transactivator (P33076).

    Function (from Uniprot):

    Essential for transcriptional activity of the HLA class II promoter; activation is via the proximal promoter. No DNA binding of in vitro translated CIITA was detected. May act in a coactivator-like fashion through protein-protein interactions by contacting factors binding to the proximal MHC class II promoter, to elements of the transcription machinery, or both. Alternatively it may activate HLA class II transcription by modifying proteins that bind to the MHC class II promoter. Also mediates enhanced MHC class I transcription; the promoter element requirements for CIITA-mediated transcription are distinct from those of constitutive MHC class I transcription, and CIITA can functionally replace TAF1 at these genes. Exhibits intrinsic GTP-stimulated acetyltransferase activity. Exhibits serine/threonine protein kinase activity: can phosphorylate the TFIID component TAF7, the RAP74 subunit of the general transcription factor TFIIF, histone H2B at ‘Ser-37’ and other histones (in vitro).

    And here are the values of the blast between the human protein and cartilaginous fish:

    Length: 1130 AAs
    Bitscore: 510 bits
    Identities: 320 (28%)
    Positives 457 (40%)
    baa: 0.45
    E-value: 4e-161

    Now, here we have two long and functional proteins, both with important regulatory functions.There is no doubt that the human and the cartilagionou fish forms are strong homologues in both cases: The E value is, of course, 0 for UBR5, but it is however a more than repsectable 4e-161 for MHC class II transactivator. The homology is beyond any possible doubt.

    But look at the different behaviour of the two proteins, not only the bitscore (4913 vs 510), which of course is also influenced by the different lengths of the two proteins, but especially the two indicators oh homology density:

    Identities: 92% vs 28%

    baa (bits per aminoacid): 1.75 vs 0.45

    The difference is amazing!

    Even more, if we consider that these are exponential values: this is not the variance of a linear measure. A bitscore of 4913 bits is incredibly higher than a bitscore of “only” 510 bits, it’s the difference between 2^510 and 2^4913, IOWs the difference between 10^153 and 10^1479!

    Again, it’s an amazing difference.

    Why is the second protein so much “less conserved” than the first?

    We don’t know exactly, because there are always two possible explanations:

    a) The protein has less functional density, IOWs is more tolerant to neutral variation.

    b) The protein undergoes some specific functional tweaking in different species.

    IOWs, we cannot easily distinguish between neutral variation and functional variation.

    However, the meaning of it all is that the homology bitscore is really measuring the functional constraints of the sequence we observe. There can be no doubt that UBR5 exhibits an amazing level of functional constraint, while the second protein has a more “normal” behaviour. If we assume that the lower bitscore in the second protein is only an expression of neutral variation, then the difference in bitscores between the two proteins is measuring very precisely the difference in functional constraints.

    IOWs, the functional information.

  109. 109
    bill cole says:

    gpuccio

    Here is my post to Corneel at TSZ. Any comments would be appreciated.

    Corneel,

    So what exactly do paragraph A, paragraph B, the 3rd paragraph of A and paragraph P represent in his example? gpuccio didn’t make it explicit and I could not think of a proper match for this analogy in protein evolution, but it appears you could.

    It could represent two protein families isolated in sequence space. The ubiquitin system and the spliceosome would be examples two systems that require very different sequences and contain proteins that are highly conserved.

    Trying to find a selectable random path between these two would be like trying to find a selectable random path between these two paragraphs.

    In both cases we are dealing with exceedingly large sequence spaces.

    Like the paragraphs, the sequences that build these protein groups require conscious intelligence to generate the observed function IMO.

  110. 110
    gpuccio says:

    bill cole:

    Yes, your ideas are correct.

    Indeed, my example with language is not so much a metaphor of protein evolution, but rather a tangible example of complex functional information, and of the reasons why it cannot be generated in an existing system by RV and NS.

    Of course, paragraph P can be compared to a new complex functional protein, or protein superfamily: any new component that appears in an existing system, and is new and original and complex.

    It can also be new and original functional information added to an existing protein: see for example the case of UBR5.

    In this case, UBR5 as it existed in pre-vertebrates would be the starting system, and UBR5 as it appears in the ancestor of cartilaginous fish and bony fish would be the system with paragraph P added to it.

    Note that the 2000+ bits of human conserved functional information that are added to UBR5 in the transition to vertebrates are well comparable to the likely functional information in paragraph P. I quote from the OP:

    Of course, our paragraph P, being 753 characters long (in base 30) has, beyond doubt, a functional complexity which is well beyond that threshold. Probably higher than 1000 bits, maybe nearer to 2000 bits.

  111. 111
    Origenes says:

    Allan Keith @

    This post is largely off-topic, but since Allan Keith is the only materialist who has put forward an argument in this thread, I would like to elucidate my point about a fluctuating environment.

    Suppose, a world without natural selection — a world with unlimited space and resources. In this world, life, driven by chance mutations, veers off in all possible directions. All viable organisms capable of reproduction will live, prosper and evolve. Clearly, such a world would lead to a maximum variety of life forms, maximum exploration of search space and innovation. It would be a world where chance rules supreme and every viable mutation becomes reality and is explored further.

    Surely, one can argue that such an ideal world cannot exist, e.g. some organisms eating each other, but, for the sake of argument, suppose that such a world, or something close to it, can exist.

    With this world in mind it’s easy to see, that every other world can only be less successful at finding innovations. Any elimination of viable organisms implies shutting down pathways.

    Natural selection in the form of a very cold winter shuts down the evolutionary pathway for all sheep except for the very woolliest sheep. For clarity, this shut-down is not the creation of woolly sheep; it is the elimination of the not so woolly sheep.
    Without a very cold winter, or a breeder selecting, the very woolliest sheep would exist also together with less woolly sheep.

    However, after a very cold winter, woolly ewes only mix with woolly males. So, selection does something: in this case, it leads to more woolly sheep. This means that selection causes a more extensive exploration of the ‘woolly sheep evolutionary pathway’. Selection results in relatively more woolly sheep and therefore more exploration of mutations in the woolly sheep genome. That’s the only thing that can be said in favor of selection.
    IOWs selection intensifies the exploration of certain evolutionary pathways at the cost of abandoning the search along other pathways.
    But what would happen if very cold winters are alternated by very hot summers? Or what if the environment is unstable and underwent constant change? Does that help evolution? Allan Keith thinks it does:

    Allan Keith: But the whole idea of isolated islands of functional space is a fallacy. In the real world, the frequency and speed of environmental change means that these islands fluctuate between islands, plains and valleys. …
    The fitness landscape is more like a stormy sea. What was insurmountable yesterday is a flat plain today and a down hill run tomorrow. …
    …. about changing environment. This is not limited to climate and other physical changes. It also includes things like population density changes, increased predation, etc.

    But the unstable world that Allan describes is clearly extremely inhospitable for evolution. A simple illustration: if the environment fluctuates between very cold winters and very hot summers no sheep will survive at all. An unstable fluctuating environment does not shut down certain evolutionary pathways in favor of others, but it only shuts down more pathways.

  112. 112
    Origenes says:

    (follow up #111)

    Allan Keith: With regard to islands of function, if it is more like a seascape than a landscape, as you have admitted, how do you continue to claim that the “search space” is insurmountable? … If a mutation (or other source of variation) results in increased fitness it will be more likely to become fixed in the population.

    No Allan, “increased fitness” in the winter (woolly sheep) is not much help if it is followed by a hot summer.

    Bottom line: For evolution to be successful it needs a stable environment that consistently leaves certain pathways open to organisms. This allows for consistent exploration of a part of the search space and ensuing adaptation over long time periods.
    An instable fluctuating environment is a nightmare for evolution.

  113. 113
    gpuccio says:

    Origenes:

    I certainly agree with you that environment fluctuations are no help in generating new functional information, and in many cases they can be an obstacle, eliminating precious solutions that are already existing.

    However, your argument abou “a world with unlimited space and resources”, even if clearly hypothetical, seems not to consider an important aspect of the question: that the expansion of any variation is fundamental to give it greater probabilistic resources. And that expansion can only be provided by NS, IOWs by the extinction of other forms of variation. Unless you are conceiving, even if for the sake of discussion, a “a world with unlimited space and resources” that can really host an exponentially growing number of organisms, infinitely expanding themselves. But that would be really absurd, even for an hypothetical argument.

    So, let’s say that at least the total number of organism, n, is limited. And let’s follow what happens to an event of RV, e.

    The point is, even if e is not subject to any NS from the environment and its fluctuations, if the number of organisms n is finite, it can only undergo one of three destinies:

    a) expand to a big population number

    b) remain limited to its original clone, IOWs to one or a few organisms

    c) be cancelled, because other clones are expanding

    Now, let’s say that the population is in a very good balance, and all new variations survive, but remain confined to their original clones. Then the number of variants will remain approximately the same at all times, because of course each new variant, like e, is also cancelling an old state (the organism where it takes place, before e).

    IOWs, n is anyway the highest number of variants that the population can host, in the limit case that each organism is different from any other.

    But if we imagine that e, for some good luck, is a trait that can get to some new function by a few other events of variation, tyhen the probabilities of getting even two or three specific coordinated variation in the organism with e are extremely low, because the population hosting e is limited to one or a few individuals. It’s only expansion of e that gives some probabilistic resources to any walk starting from e.

    So, let’s say that e is neutral. Will it expand?

    The concept of drift tells us that it can expand, but that its probabilities to expand are not higher than the probabilities of any other neutral variation that is in the population.

    So, a few neutral variations will expand, in time, and therefore acquire more significant probabilistic resources, but most neutral variations will be cancelled by those processes of random fixation.

    And the environment has no role in all that, except for the very obvious quality of not being infinite.

    My point is: in an environment which if finite, even if we do not consider any other effect of the environment itself, the powers of RV are however extremely limited, and some form of neutral and random selection (drift) however takes place.

    NS as conceived by darwinists becomes important only for variations (in existing traits) which change significantly the reproductive success in the existng environment, however stable or unstable it is. The role of NS is important in its negative form (eliminating variations that compormise reproduction), because that effect is strong and preserves existing function. We see it in all conserved protein sequences.

    Instead, the effect of positive selection (expanding a fixing a new variation for its positive effects) can be seen in extremely rare cases, and always when the environment becomes extremely hostile to some already existing condition (see for example antibiotic resistance). And of course it always act on simple variations.

    Another case could be when “positive” selection can favour some complex species vs another existing complex species: for example, the extinction of one species for some environmental change can help the expansion of another existing complex species. But the complex species that expands nust already existi, and the environments change does not help in any way to explain how that complex species came into existence.

    The problem with NS is always the same: it can only act on functions that already exist. If the function is extremely simple, it can in some cases exist because RV generated it (see antibiotic resistance). But if the function is complex, RV could never have generated it.

  114. 114
    Origenes says:

    GPuccio @113

    GP: I certainly agree with you that environment fluctuations are no help in generating new functional information, and in many cases they can be an obstacle, eliminating precious solutions that are already existing.

    “In many cases”, you say, but I cannot envision a case of a fluctuating environment being not a hindrance to evolution — a cold winter eliminates not so woolly sheep and a hot summer eliminates woolly sheep.

    GP: However, your argument about “a world with unlimited space and resources”, even if clearly hypothetical, seems not to consider an important aspect of the question: that the expansion of any variation is fundamental to give it greater probabilistic resources. And that expansion can only be provided by NS, IOWs by the extinction of other forms of variation.

    Indeed, I do want that consideration off the table. I want the reader to consider a world without NS, with unlimited space and unlimited probabilistic resources for every organism. Why? Because it illustrates the obvious point that a world without NS is ideal for evolution.
    I wrote: “… selection intensifies the exploration of certain evolutionary pathways at the cost of abandoning the search along other pathways.” In my proposed hypothetical world no search needs to be abandoned. Again, the point is obvious: a world without NS is ideal for evolution.
    This point needs to be made, because many Darwinians seem to think that it is a great thing to have NS around — see e.g. the Darwin quote in post #99.

    GP: Unless you are conceiving, even if for the sake of discussion, a “a world with unlimited space and resources” that can really host an exponentially growing number of organisms, infinitely expanding themselves. But that would be really absurd, even for an hypothetical argument.

    Okay, you reject my proposal of this world, so I cannot make my point along this line. That’s fine; we do not have to agree on everything. 🙂

  115. 115
    gpuccio says:

    Origenes:

    “Okay, you reject my proposal of this world, so I cannot make my point along this line. That’s fine; we do not have to agree on everything.”

    OK, that’s fine with me too! 🙂

    But, leaving apart your argument, I still would like to emphasize a few points about the environment, its changes, and NS.

    The important point is: most NS has nothing to do with the environment, least of all with its changes.

    For example, let’s tale negative selection, what darwinists also like to call “purifying selection”.

    It’s by far the most common observable form of NS. I just elimimates the variation that compromises function, and therefor like and reproduction.

    It’s the reason why we see highly conserved sequences in proteins, even if certainly a lot of mutations must have happened in the course of natural history. The simple point is: those mutations were eliminated, because they had a negative effect on function, life and reproduction.

    Now, environment has nothing to do with that. I a mutation causes the loss of asome basci function in the cell, and the cell dies, what has the environment to do with that? Least of all, environmental changes?

    Of course, the selecting factor here is life itself, its rules, its basic organization and working.

    But even the acquisition of some new function that can be selected is not necessarily linked to the environment and to its changes. Many of them are useful for the same reasins that negative variation is negative: they make the organization of life more functional.

    Let’s take the ubiquitin system, and all its complex organization. Let’s say that it originates in eukaryotes. Is it directly linked to environment, and to its chabges?

    I would say that that that is not the case. The ubiquitin system is a complex regulatory system. Its necessity comes from the existence itself of the eukaryotic cell, with all its new functions and inner organizations, which require a new level of control on proteins and their concentration in the different parts of the cell at different times, and on the many signaling pathways that rule in the eukaryotic cell.

    Again, new functions are necessary to implement and control the new complexity. The environment is not the cause of that.

    My point is: most of the functions we observe in living organisms are intrisic to the establishment and maintenance and functional development of life itself. The environment, and its changes, has only a permissive role, very indirect.

    In most cases, it’s the rules themselves of function and complexity that select, both negatively and positively.

  116. 116
    Origenes says:

    GPuccio: … most NS has nothing to do with the environment, least of all with its changes.
    For example … “purifying selection”. It’s by far the most common observable form of NS. I just elimimates the variation that compromises function, and therefor life and reproduction.

    Now, environment has nothing to do with that. If a mutation causes the loss of some basic function in the cell, and the cell dies, what has the environment to do with that? Least of all, environmental changes?

    Of course, the selecting factor here is life itself, its rules, its basic organization and working.

    Thank you for pointing this out. Perhaps “existential selection” is also an appropriate term. One thing is for sure: it should be kept separate from “environmental selection.”
    At the most basic level “existential selection” selects between viable and non-viable organisms. And in general it could perhaps be said that it selects for the internal coherence of the organism; indeed independent from the external environment.

  117. 117
    LocalMinimum says:

    Origenes @ 111:

    Suppose, a world without natural selection — a world with unlimited space and resources. In this world, life, driven by chance mutations, veers off in all possible directions. All viable organisms capable of reproduction will live, prosper and evolve. Clearly, such a world would lead to a maximum variety of life forms, maximum exploration of search space and innovation. It would be a world where chance rules supreme and every viable mutation becomes reality and is explored further.

    Excellent example. Remove the illusion of “selective promotion” by removing selection.

    Natural selection is the purest critic, never an artist. And a dumb and uninspired critic, at that.

  118. 118
    DATCG says:

    Another good post for understanding limitations of blind evolution Gpuccio, well done.

  119. 119
    gpuccio says:

    DATCG:

    Thank you.

    I think that it is very important to see things really: concepts become much more real, when we can see objects that implement them with our own eyes.
    I am also very happy that I could find this new champion protein, the E3 ligase UBR5. It’s really amazing.

    Just to see things with our own eyes even more in detail, I have blasted the human protein against fish (both cartilaginous and bony). As usual, the blast page gives as default the 100 best alignments of the human protein with fish proteins.

    The best bitscores were those of callorhincus milii ( a shark) and Lepisosteus oculatus (a bony fish), practically the same:

    4913 and 4910 bits

    But all the 100 alignments were comparable, the lowest of all them being the one with an isoform in Cynoglossus semilaevis (a bony fish):

    4730 bits

    So, all 100 fish proteins had bitscores between 4730 and 4913 bits.

    I have also activated the tool for a multiple alignment of those 100 hits (COBALT).

    The result is really impressive. Can you imagine how many AAs are identical to those in the human protein in all 100 fish proteins considered?

    The answer is: 2225!

    This is, of course, a much greater functional specificity than my paragraph P, which has been so useful in showing how RV + NS can never, never explain that kind of results.

  120. 120
  121. 121
    gpuccio says:

    Mung:

    Yes, I have read it. Hunter’s ideas here are certainly very similar to mine.

    I have also checked the paper referenced there. Centrobin seems another interesting protein.

    However, the protein in drosophila is scarcely related, at sequence level, to the protein in humans, even if they are certainly homologues (E value = 1e-12).

    Centrobin seems to be one of those proteins that find the human specific sequence only late, indeed at the level of mammals. Up to reptiles, the protein is still very different from the mammalian form.

  122. 122
    DATCG says:

    Gpuccio @119,

    The result is really impressive. Can you imagine how many AAs are identical to those in the human protein in all 100 fish proteins considered?

    ummmm… well you know IDist have no imagination 🙁


    “The answer is: 2225!”

    Oh My! Imagine that! 🙂

    This is, of course, a much greater functional specificity than my paragraph P, which has been so useful in showing how RV + NS can never, never explain that kind of results.

    ImagineThat**2 ! 😉

    But… uh panspermia, hgt… you know, just imagine! 🙂 Darwinist have us beat in the imaginary story-telling I guess. sigh…

    Haha, OK, if you see this, do you mind reposting your BLAST How-To link?

    I used it many months ago, but have lost the link.

    Thanks!

  123. 123
    gpuccio says:

    DATCG:

    Here it is:

    Bioinformatics tools used in my OPs: some basic information.

    https://uncommondescent.com/intelligent-design/bioinformatics-tools-used-in-my-ops-some-basic-information/

  124. 124
    gpuccio says:

    DATCG:

    I have checked with greater precision, and the total number of identical AAs in all the 100 alignments with fish proteins for UBR 5 is:

    2227

    However, the total number of AAs that are identical in more than 90% of the aligned sequences is:

    2668

    That’s 95.3% of the whole protein.

  125. 125
    bill cole says:

    gpuccio

    Here is an interesting paper on historically large information adds.
    https://www.nature.com/articles/s41467-018-04136-5.pdf

  126. 126
    gpuccio says:

    bill cole:

    That seems really interesting, and not so different from what I am trying to do! Thank you for linking that paper. 🙂

    If I had to list the greatest information jumps in natural history, they would definitely be:

    1) OOL

    2) Origin of single celled eukaryotes

    3) Origin of Metazoa

    4) Origin of vertebrates

    Well, there are certainly many others, but these are really the first that come to mind.

    Each of those transitions is a real information “miracle” (if you allow me the word! 🙂 )

    I will read the paper with deep attention, and see if there is something that can be commented upon in more detail. Thank you again.

Leave a Reply