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Author Topic:   Another IDology challenge -- complete with complaints of harsh treatments ...
PaulK
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Posts: 15395
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Message 46 of 60 (861938)
08-29-2019 2:14 PM
Reply to: Message 45 by WookieeB
08-29-2019 1:36 PM


Re: more filling in the blanks.
Axe’s 10^-77 figure is almost certainly too low, and also irrelevant to most of evolution. If you remember it was discussed in this thread:Exposing the evolution theory. Part 2

This message is a reply to:
 Message 45 by WookieeB, posted 08-29-2019 1:36 PM WookieeB has not yet responded

    
WookieeB
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Posts: 82
Joined: 01-18-2019


Message 47 of 60 (861941)
08-29-2019 2:32 PM
Reply to: Message 19 by RAZD
08-25-2019 9:39 AM


Re: more filling in the blanks.
Wookieeb writes:

What are you talking about? What is a "void in habitat"? ...

RAZD writes:

A void is an empty niche in the ecology.


Arghh! What are you talking about?!?
You are equivocating words here. So is a "void" [in habitat] the same as an "empty niche" [in the ecology]? I'm taking "void" and "empty niche" to be synonymous. But is "habitat" a synonym for "ecology*"? Doesn't seem so with your "ecology" definition:
The ecology is composed of all species in a habitat in a quasi-balance of survival and reproductive abilities, not just in predator-prey arms races but also in like species competitions.

I think you mean ECOSYSTEM (as any *ology means: study of *), but otherwise I'm fine with your definition of "ecology". But per your definition "ecology" and "habitat" are clearly different, so a "void" in either is not the same thing. Also the "species" and "habitat" are not synonymous, though related in your description.

So what again is the "void" or "empty niche" supposed to be? You haven't defined it, and I'll have to try to reason it out based on your statement above. If I go off them, since the "ecology" is equivalent to the all species in a habitat, then a void/empty niche would have to be a lack of or not existing species in a habitat. But that doesn't make much sense. Evolution has no awareness of a lack of species. It has no forward vision. It cannot plan for a not-yet existing species.

Thanfully, you leave the idea of a empty niche in "ecology" in your next statement and go back to talking about the habitat:

If one of the species can take advantage of a new habitat niche that is not currently occupied then it has more resources for survival and reproduction than previously, giving it an advantage.

So now you are leaving species aside and talking about a "habitat [empty] niche". I'm guessing this habitat is more where you intend your focus. A habitat niche I can understand, as it would relate to how an organism/species relates to its environment. In that sense, EVERY species has its own niche. But a void/empty niche is an empty set, being either 1) how an existing species does not relate to it's environment (nonsensical) or 2) a non-existing species interacting in an environment, which is not possible. In other words, a void/empty niche in a habitat isn't a thing.

As a variation on (1) above, if you are trying to describe this as some set of potential or imaginary species that could relate to the environment in a way different from all other species, then fine, but you need to find a new word. But that set would be nearly infinite in the imagination as one could imagine just about any organism that does something different. And yet that set is not real. Either way, you're referring to something that is a goal, or possibility. But evolution does not reach for a goal, it doesn't imagine anything ahead.

So an empty niche doesn't exist (it's merely a concept), and a niche exists as a(ny) species interacting in the environment. The number of actual niches is equal to the number of species in existence.

Unless you have a different or more strict definition of your void/empty niche, you're statement ends up being a nonsense tautalogy.

This is actually observed in the case of foraminifera:

They are using the terms species and evolution quite loosely in this article. It doesn't seem to fit standard usage of terms, and they seem to offer contradicting ideas at times (see last paragraph). In all, there is not much here that is really a noteworthy example of evolution in a Neo-Darwinian sense. There talking about forams the whole way through, with changes that I would just consider normal diversification (like the many dog breeds, or even humans). Either way, it's the type of evolution that is no problem and even the most ardent critics of Darwinism would accept. The end is a bunch of speculation and a vague mention of 'niches'. (that where you got the term from?)

Similarly, the Cambrian "explosion" of new species types that first evolve protective shells occurred because the niche for species with protective shells was empty.

Please! Evolution occurred because it saw a potential opening niche? With no explanation for the new information needed to build the new body forms and organ types, and no precursors evident?

Let's start with this definition of evolution as a process:

The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities for growth, development, survival and reproductive success in changing or different habitats.

About as vague and broad a definition as you could get. Basically: things change. Ok. I agree. This "evolution" happens.....
But it's missing the details regarding some proposed changes/differences between organisms in life. How and why specifically? No mention of where the information required for developing major differences comes from, nor how to explain getting around the apparent limits of adaptation within species?


This message is a reply to:
 Message 19 by RAZD, posted 08-25-2019 9:39 AM RAZD has responded

Replies to this message:
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RAZD
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Posts: 20120
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


(1)
Message 48 of 60 (861986)
08-30-2019 11:05 AM
Reply to: Message 44 by WookieeB
08-29-2019 1:18 PM


Re: more filling in the blanks.
There are a couple themes being discussed here and I can get fairly verbose in responding, ...

So can I, so it will take me a while to answer all your posts.

First off, pretty much nobody (that I know of) says that speciation is impossible, or never happens. ...

ummmm ... the whole point of the video was to show through math that it was virtually impossible, therefore intelligent (eg god) design.

... Secondly, a lot of this also depends on what one uses as a definition of "speciation". If the definition is complete reproductive isolation, then most of your cited examples don't fit.

Biologists recognize that speciation is muddy, especially when discussing anagenesis, or arbitrary speciation in a single lineage.

quote:
Anagenesis suggests that evolutionary changes can occur in a species over time to a sufficient degree that later organisms may be considered a different species, especially in the absence of fossils documenting the gradual transition from one to another.[8] This is in contrast to cladogenesis—or speciation in a sense—in which a population is split into two or more reproductively isolated groups and these groups accumulate sufficient differences to become distinct species. ...

Controversy arises among taxonomists as to when the differences are significant enough to warrant a new species classification: Anagenesis may also be referred to as gradual evolution. The distinction of speciation and lineage evolution as anagensis or cladogenesis can be controversial, and some academics question the necessity of the terms altogether.[21][22][23]


There are many cases where different species are recognized where complete reproductive isolation has not occurred. Generally this happens when behavior in mate selection operates to maintain breeding population isolation even though hybrids are possible. Note that a definition of species was given in the quote:

message 19 writes:

quote:
Over the last few decades the theoretically preeminent species definition has been the biological species concept (BSC). This concept defines a species as a reproductive community.

This recognizes that behavior can isolate populations even though hybrids are possible. See Wildebeests discussion in Message 41.

Your main examples come in the fashion of hybridization. Hybridization, I agree can produce something that falls under the definition of speciation (and I would include a couple plants from your 'list'), but then hybridization does not fall under the processes normally associated with the 'standard evolutionary model'. The standard evolutionary model would basically be the normal Darwinian/Neo-Darwinian process of mutation and natural selection. Hybridization (even via polyploidy) is not via that sort of process.

No, the standard evolutionary model would include all the known processes of evolution. That's why I didn't say "Darwinian/Neo-Darwinian" but evolutionary.

Further, polyploidy is a mutation process, and hybridization is also reproduction and mate selection, no different than mixtures of varieties within a species.

And this critcism doesn't address:

Message 19 writes:

quote:
5.2 Speciations in Plant Species not Involving Hybridization or Polyploidy

5.3 The Fruit Fly Literature

5.4 Housefly Speciation Experiments

5.5 Speciation Through Host Race Differentiation

5.6 Flour Beetles (Tribolium castaneum)

5.7 Speciation in a Lab Rat Worm, Nereis acuminata

5.8 Speciation Through Cytoplasmic Incompatability Resulting from the Presence of a Parasite or Symbiont


The point is that biologists have recognized speciation in a multitude of instances.

The Neo-Darwinian process is what Gelernter was referring to in the phrase you quoted. So I do not agree with you that his statement was "misinformation" or incorrect. Of course, if you want to quibble about definitions, we can. But from the context it is pretty clear on what Gelernter was referring, since he even made a differentiation between what he called "the small adjustments by which an organism adapts to local circumstances" or "the fine-tuning of existing species" with "the origin of species" (which would all fall under your definition of Evolution", vs how a Darwinian process can explain the differences. He's making a distinction that you haven't really acknowledged yet.

This type of "distinction" is also typical creationist/IDologist semantic misdirection -- which is why it is misinformation. Anytime you see the words "Darwinian" or "Neo-Darwinian" you can be pretty sure that the author is equivocating between a vary narrow view of some evolutionary processes and the full band-width of all known evolutionary processes. Pretending/implying they are the same means making the "part for the whole" logical fallacy.

As for speciation via hybridization, it is rather an underwhelming example to showcase your evolution. Even under an evolutionary paradigm, hybridization would likely be looked at as two species that had recently diverged coming together and making a hybrid. If that was the case, you are looking at really a loss or decrease of genetic diversity instead of adding new stuff.

Sadly, this is incomplete. The hybrid combines traits that have evolved independently in the recently diverged daughter populations. This hybrid process goes through several stages as the daughter species diverge. Initially you get Heterosis:

quote:
Heterosis, hybrid vigor, or outbreeding enhancement, is the improved or increased function of any biological quality in a hybrid offspring. An offspring is heterotic if its traits are enhanced as a result of mixing the genetic contributions of its parents. These effects can be due to Mendelian or non-Mendelian inheritance.

Early hybrids can be better fit than either parent population, but later hybrids can result in less fit offspring (again see Wildebeests discussion in Message 41).

From Population Dynamics - the math behind the evolution of species, Message 6 regarding the development of sexual incompatibility:

quote:
The population genetics of speciation: the evolution of hybrid incompatibilities.

The central assumption of the DOBZHANSKY-MULLER model of speciation is that alleles cause no sterility or inviability on their normal "pure species" genetic background. Instead, an allele can lower fitness only when brought together with genes from another species. Any particular hybrid incompatibility might cause partial or complete hybrid sterility or inviability. For most of this paper, I assume that hybrid incompatibilties involve interactions between pairs of genes, as in DOBZHANSKY and MULLER'S verbal models. Later, I consider three-locus and higher interactions. I also assume that multiple substitutions do not occur at the same locus, an assumption that is reasonable during the early divergence of taxa. I assume nothing about the evolutionary causes of substitutions. The DOBZHANSKY-MULLER model of speciation requires only that substitutions occur and assumes nothing about whether they are brought about by natural selection or genetic drift.

Because I consider the cumulative effects of interactions between many loci -- which quickly gets complicated -- it is useful to picture this process diagramatically. Figure 1 offers a simple way to picture the accumulation of complementary genes between two haploid populations. Each of the two heavy lines represents a lineage descended from a common ancestor. The two allopatric populations begin with identical "ancestral" lowercase genotypes at all loci (a b c . . .). Time runs upward, with the first substitution occurring at the a locus, the second at the b locus and so on.


As time in isolation passes the incompatibilities build up and the offspring become less viable. The reason that breeders cross-breed varieties/species is to mix new stuff and create a better breed. Corn for example.

The specific cases of Tragopogon mirus and Galeopsis tetrahit are probably legitimate forms of speciation via polyploid hybridization. But it's all meh, since this only occurs within flowering plants, it relies on pre-existing parent species, and there isnt really any new morphological characteristics.

Heliconius butterfly hybrids don't really fall into it this category because it doesn't appear that this is a case of reproductive isolation. It is more accounted for by interbreeding with various lines (including old parental/generational).

Moving the goal-posts? You asked for examples of speciation, you got examples of speciation. That they aren't different enough to meet your expectations just means your expectations were erroneous.

quote:
Hybrid (biology)

Species are reproductively isolated by strong barriers to hybridisation, which include morphological differences, differing times of fertility, mating behaviors and cues, and physiological rejection of sperm cells or the developing embryo. Some act before fertilization and others after it. Similar barriers exist in plants, with differences in flowering times, pollen vectors, inhibition of pollen tube growth, somatoplastic sterility, cytoplasmic-genic male sterility and the structure of the chromosomes. A few animal species and many plant species, however, are the result of hybrid speciation, including important crop plants such as wheat, where the number of chromosomes has been doubled.


Speciation has occurred, it has been observed, it is fact.

All the other examples in your list I would not consider speciation, since the reproductive isolation has not been established in those examples.

What you consider is irrelevant, the issue is what biologists consider, and they consider speciation to be observed to occur.

All in all, even though I would concede that speciation (within some limits) via Darwinian processes is possible, but this still has not been demonstrated by your examples. Despite all of this the bigger question remains: this is still not demonstrating anything akin to being able to explain the macro level differences between most organisms.

That is your opinion, and not one shared by biologists. Speciation increases diversity and allows for more evolution to occur in following generations that further differentiates the daughter species. All evolution occurs at the breeding population level by standard evolutionary processes. Macro-evolution is just the accumulation of these generational changes over multiple generations.

Enjoy


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by our ability to understand
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This message is a reply to:
 Message 44 by WookieeB, posted 08-29-2019 1:18 PM WookieeB has responded

Replies to this message:
 Message 55 by WookieeB, posted 09-19-2019 6:35 PM RAZD has responded

  
Taq
Member
Posts: 8012
Joined: 03-06-2009
Member Rating: 4.6


(1)
Message 49 of 60 (861998)
08-30-2019 12:59 PM
Reply to: Message 45 by WookieeB
08-29-2019 1:36 PM


Re: more filling in the blanks.
WookieeB writes:

How are you justifying that the 10^77 number is fabricated? Cause you don't like it?

It is fabricated because it hasn't been empirically tested. It is a fabrication of the assumptions Axe makes.

However, we can test Axe's calculations empirically. VDJ recombination during B-cell development produces billions B-cell lineages each with their own antibodies. The variable region of these antibodies can serve as a model for finding function. In fact, we can see if any of those antibodies have B-lactamase activity, the function that Axe says can only occur once in every 1x10^77 combinations.

quote:
Here we report the construction of a large murine single chain fragment variable (scFv) phage display library of size 2.7 × 10^9 with extended diversity by combining different mouse models. We have used two molecularly different inhibitors of the R‐TEM β‐lactamase as targets for selection of catalytic antibodies with β‐lactamase activity. This novel methodology has led to the isolation of five antibody fragments, which are all capable of hydrolyzing the β‐lactam ring.
https://febs.onlinelibrary.wiley.com/...l/10.1111/febs.14012

In a library of 2 x 10^9 random peptides they were able to find 5 of those random peptides that had B-lactamase activity, well below the number given by Axe. Even if we look past all of the problems with Axe's mathematical model, reality shows us that Axe is wrong by many orders of magnitude.


This message is a reply to:
 Message 45 by WookieeB, posted 08-29-2019 1:36 PM WookieeB has responded

Replies to this message:
 Message 56 by WookieeB, posted 09-19-2019 7:04 PM Taq has responded

  
RAZD
Member
Posts: 20120
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


(1)
Message 50 of 60 (862003)
08-30-2019 1:16 PM
Reply to: Message 45 by WookieeB
08-29-2019 1:36 PM


probabilities and possibilities
I'm going to make 2 replies here, the first to one statement to hammer home a point:

I have two di -- a pair of dice -- what is the probability that I will throw/roll a seven in one try?

The answer to the die question is: 1 in 6

This exemplifies the trouble with assumptions. You assumed two six sided di, when there are five types of regular polyhedra di (used in dungeons and dragons games, etc):

  1. Four sided (tetrahedron)

    1234
    12345
    23456
    34567
    45678

    7's: 2 out of 16

  2. Six sided (hexahedron)

    123456
    1234567
    2345678
    3456789
    45678910
    567891011
    6789101112

    7's: 6 out of 36

  3. Eight sided (octahedron)

    12345678
    123456789
    2345678910
    34567891011
    456789101112
    5678910111213
    67891011121314
    789101112131415
    8910111213141516

    7's: 6 out of 64

  4. Twelve sided (dodecahedron)

    123456789101112
    12345678910111213
    234567891011121314
    3456789101112131415
    45678910111213141516
    567891011121314151617
    6789101112131415161718
    78910111213141516171819
    891011121314151617181920
    9101112131415161718192021
    10111213141516171819202122
    11121314151617181920212223
    12131415161718192021222324

    7's: 6 out of 144

  5. Twenty sided (icosahedron)

    1234567891011121314151617181920
    123456789101112131415161718192021
    2345678910111213141516171819202122
    34567891011121314151617181920212223
    456789101112131415161718192021222324
    5678910111213141516171819202122232425
    67891011121314151617181920212223242526
    789101112131415161718192021222324252627
    8910111213141516171819202122232425262728
    91011121314151617181920212223242526272829
    101112131415161718192021222324252627282930
    111213141516171819202122232425262728293031
    121314151617181920212223242526272829303132
    131415161718192021222324252627282930313233
    141516171819202122232425262728293031323334
    151617181920212223242526272829303132333435
    161718192021222324252627282930313233343536
    171819202122232425262728293031323334353637
    181920212223242526272829303132333435363738
    192021222324252627282930313233343536373839
    202122232425262728293031323334353637383940

    7's: 6 out of 400

    Total 7's: 26 out of 660

And this doesn't count pairing 4&6 (4/24), 4&8 (4/32), 4&12 (4/48), 4&20 (4/80), 6&8 (6/48), 6&12 (6/72), 6&20 (6/120), 8&12 (6/96), 8&20 (6/160) and 12&20 (6/240) sided di, for 78 out of 1580 possibilities, or about 1 in 20.

Nor does it account for non-regular polyheda di that can vary from 2 to ∞ and the probability → 0

Your mathematical model failed because it made an invalid assumption that limited the ability of the model to reflect reality.

My point being that you must know all the possibilities before you can estimate the possibilities. If you assume a limited number of possibilities and your model fails to reflect reality, then reality is not the problem -- the model is the problem, the assumption/s in the model are the problem.

Math is not capable of invalidating or changing reality. Learn this if you learn nothing else from this thread.

Enjoy

Edited by RAZD, : Arrow code


we are limited in our ability to understand
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Rebel•American•Zen•Deist
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This message is a reply to:
 Message 45 by WookieeB, posted 08-29-2019 1:36 PM WookieeB has responded

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RAZD
Member
Posts: 20120
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


(2)
Message 51 of 60 (862010)
08-30-2019 3:34 PM
Reply to: Message 45 by WookieeB
08-29-2019 1:36 PM


impossible probabilities and bogus possibilities
As for you linked postings, I'm not seeing how it relates unless you can be more specific about where the problem is. Your listing is rather vague on it's own, but here is how I would comment on each numbered point with regards to the OP.

With reference to the old improbable probability problem (posted in 2004):

1) Um, ok, duh!. Language is odd, as a model of reality is a model of reality. A model of reality NEVER replicates reality, it merely describes reality. So if the reality doesn't conform to the model, no duh, the model is wrong (is missing something).

Good start -- now apply that to Gelernter's model and the fact that speciation has occurred and therefor reality has shown his model to be invalid.

2) irrelevant. We're not referring to the formation of life. But if you want to argue semantics, than yes, this probability is considering all possible pre-existing molecules within the context of what is being discussed.

quote:
2. The calculation fails to account for the known pre-existing molecules used in the formation of life that are found throughout the universe, and this failure means the calculation with creation-all-at-once including these molecules is unnecessarily extended downward, starting with too much simplicity.

And this applies to how molecules are actually assembled by cells, rather than the single simplistic manner described by Gelernter et al.

3) doesn't apply.

quote:
3. The calculation fails to account for the fact that the first life need not be as complicated as a modern cell, that the minimum configuration is much simpler as shown by the LUCA studies. This failure means that the calculation is unnecessarily extended upward, ending with too much complexity.

The first life was much simpler than what we see today, even in single cell life forms. This means that his assumed length of assembled proteins is likely much higher than necessary for early life. Later life is built on the existing life by adding and subtracting (mutations) and not by de novo development.

4) Nope. The probability calculation is specifically accounting for the combination of molecules related to it's subject. It is accounting for the combination process (that's kinda a central part of it). ...

quote:
4. The calculation fails to account for combinations of groups of such molecules in smorgasbord fashion instead of in assembly line fashion all at once all from nothing. And further, that all those "failed" experiments are still available to be cut and reassembled into new experiments without having to go through all the preliminaries. It fails to account for actual combination process as used in natural assembly of large organic compounds. Amino acids are assembled into larger molecules like peptides and not from extending amino acids by adding atoms. This failure means that all the ways to reach the final necessary combination are not included and thus it unnecessarily excludes possible combination methods.

Can you point out specifically where he/they talk about combinations other than adding one at a time? I've been through the video 3 times and read your link and I fail to see it. Link/quote to the combination of two long strands into one longer strand would be a good starting point.

...And just FYI, your mention of peptides is way off. Peptide refers to a bonding type between amino acids, and in nature it occurs about 1 in 2 times (1/2 would be peptide bonds, 1/2 would be non-peptide bonds). But for a protein to work, all the bonds have to be peptide bonds. So if you really want to highlight the peptide bond type, you are adding an additional 10^45 probability to what we already are discussing.

quote:
Peptides (from Greek language πεπτός, peptós "digested"; derived from πέσσειν, péssein "to digest") are short chains of amino acids linked by peptide (amide) bonds.[1] The simplest peptides are dipeptides, followed by tripeptides, tetrapeptides, etc. A polypeptide is a long, continuous, and unbranched peptide chain. Hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides and polysaccharides, etc.

Peptides are distinguished from proteins on the basis of size, and as an arbitrary benchmark can be understood to contain approximately 50 or fewer amino acids.[2][3] Proteins consist of one or more polypeptides arranged in a biologically functional way, ...


Peptides are intermediate in size between amino acids and proteins.

5) This does relate to the probability discussion, but not in a way you think it might. Ya, with the lottery there are a lot of possible ticket combinations and finding a win per ticket (single event) is a low probability. But there is a high certainty of a win event due to the number of tickets bought (events that occur). The same principle kinda applies, but instead we are taking about 10^195 lottery tickets produced, and the rate of winning is 1 in 10^77 tickets, which is very low The problem is though, how many tickets have actually been bought? Even if you consider a trillion (10^12) tickets bought, that even one winner exists is still extremely low. How many tickets have been actually bought is the key question here, and with evolution the answer is (comparatively) very low.

quote:
5. The probability of winning a lottery by any one ticket is extremely low, but the probability that the lottery will be won is extremely high. How do you reconcile these two very disparate probabilities? By knowing that any one of the millions of tickets is a valid winner if picked. To show that this is not the case for the calculations mentioned (ie -- in order to say "1 out of") you have to show that no other combination works of all the other probabilities. ...

We observe speciation that has occurred and that is in the process of occurring. That is reality, and it shows that the mathematical model based on large numbers is invalid. This is also the point of Message 50: the assumptions in the model are the problem.

6) The funny thing here is you complained about a model not fitting to reality, and here you go creating such a model. With regards to the probability Gelernter is mentioning, nobody is saying it is technically impossible. But for all practical purposes, if you have a 10^77 chance, with a limited # of events occurring, plus you have to hit this probability multiple times..... it is considered effectively impossible.

quote:
6. Finally, the improbability of a thing occurring is not proof of impossibility of it occurring. It could well be that this is the only planet in all the universe that has life on it because it is a very improbably event. And if you divide the surface of the planet into all the different types of environments and do the same for all the other planets and moons and asteroids in the solar system alone you will have billionsXbillions of little experimental crucibles for carrying out experiments ...

The point is that if it is an extremely low probability event, we are here and able to have this discussion because this was the winning ticket.

How are you justifying that the 10^77 number is fabricated? Cause you don't like it?

It is fabricated because it makes a limited assumption of the myriad different ways molecules are actually combined in reality. And just like the limited assumption you made on the pair of dice probability the resulting number is invalid.

No, the numbers are NOT referring to a specific type of mutation. It's not really talking about how mutations occur at all. This cements with me that you do not understand the argument.

Curiously you have yet to convince me that they discuss any other kind of mutation than a single replacement one. I haven't seen a single reference or example of a different kind of mutation. They talk about 150 AA's assembled one by one. There are 20 amino acids used and 20^150 = 1.4 x 10^195: that is for a one + one + one etc. calculation, used to estimate the number of possible combinations. The numbers match.

This means my argument in Message 3 shows that the number used by Gelernter et al. is bogus and doesn't represent real possibilities for the biological formation of proteins etc.

The argument is saying that for any modest sized protein of 150 AA's (which is 10^195 possibilities), the estimate is 1 in 10^77 will result in a functional fold (whatever function that protein then exibits). And since there are multple proteins needed for life whose sequences are wildly differentiated from each other (granted most are larger than 150 AA's), within the time span known for life on Earth (let alone even the entire age of the universe), the odds of hitting on functional proteins is exceedingly small, effectively 'impossible'.

And these numbers are based on limiting assumptions that don't reflect reality. You can also start by joining two protein fragments to form a complete protein, as noted in Message 3:

Let's cut that 150 AA protein in half -- each half then, each 75 AA segment, has a 1 in 20^75 = 3.8x10^97 possibility to assemble by their argument. Now reassemble them: there is a 1 in 4 chance of making the "right" connection (ignoring the possibility that other combinations are also functional), so that's:

(3.8 x 10^97 + 3.8 x 10^97)/4 = 1.9 x 10^97 ... half their number.

repeat for each half segment and you get:

Each quarter segment would have a 20^37.5 = 6.1 x 10^48

and {(6.1 x 10^48 + 6.1 x 10^48)/4 + (6.1 x 10^48 + 6.1 x 10^48)/4}/4 = 1.5 x 10^48 ... one quarter of their number and well below the 1 x 10^77 number they give for possible functional proteins.

Do it again for eighth segments and you get 20^18.75 = 2.5 x 10^24 for each segment and

{{(p1/8 + p1/8)/4 + (p1/8 + p1/8)/4}/4 + {(p1/8 + p1/8)/4 + (p1/8 + p1/8)/4}/4}/4 = 6.2 x 10^23

and that's not the only way those 1/8th segments could combine to make the target protein. In other words the possibilities are much higher than their model, and that is why they fail to model reality.

But that's not all, if I were to discuss the possibilities of life developing proteins I would start with the simplest known type and then look at how actual more complex proteins are developed by modification rather than assembly de novo. That way you start with functioning proteins and select new functional proteins by evolution.

quote:
The smallest protein

... TRP-Cage, a protein with only 20 amino acids derived from the saliva of Gila monsters.

Trp-cage - smallest protein

You can find the structure file and images in the PDB database (www.pdb.org) with PDB ID = 1L2Y. This highly stable mini-protein is important for studies of protein stability, protein folding, and 3D structure.

Even with this small size, it displays secondary structural elements, such as an alpha helix, found in many proteins. So far there are no known proteins with less than 20 residues, but we'll see what happens in the future.


And 20^20 = 1.0 x 10^26. Quite a different story, even using their own argument/calculation method.

The earliest life-forms would likely have the simplest proteins. Later life would have more complex proteins made by modifying existing ones.

The numbers game is one big failure after another for both creationists and IDologists.

Enjoy

Edited by RAZD, : .

Edited by RAZD, : .


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RAZD
Member
Posts: 20120
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


Message 52 of 60 (862025)
08-30-2019 4:31 PM
Reply to: Message 47 by WookieeB
08-29-2019 2:32 PM


Re: more filling in the blanks.
Wookieeb writes:

What are you talking about? What is a "void in habitat"? ...

RAZD writes:

A void is an empty niche in the ecology.


Arghh! What are you talking about?!?
You are equivocating words here. So is a "void" [in habitat] the same as an "empty niche" [in the ecology]? I'm taking "void" and "empty niche" to be synonymous. But is "habitat" a synonym for "ecology*"? Doesn't seem so with your "ecology" definition:
The ecology is composed of all species in a habitat in a quasi-balance of survival and reproductive abilities, not just in predator-prey arms races but also in like species competitions.

I think you mean ECOSYSTEM (as any *ology means: study of *), but otherwise I'm fine with your definition of "ecology". But per your definition "ecology" and "habitat" are clearly different, so a "void" in either is not the same thing. Also the "species" and "habitat" are not synonymous, though related in your description.

So what again is the "void" or "empty niche" supposed to be? You haven't defined it, and I'll have to try to reason it out based on your statement above. If I go off them, since the "ecology" is equivalent to the all species in a habitat, then a void/empty niche would have to be a lack of or not existing species in a habitat. But that doesn't make much sense. Evolution has no awareness of a lack of species. It has no forward vision. It cannot plan for a not-yet existing species.

You have a house inhabited by a variety of furniture except for one room that has no furniture. The habitat is the house, the empty room is a void that is unoccupied by furniture. The furniture in the house is an ecosystem and the empty room is an empty niche. Simplistic but should help define the point: there is space in the empty room that could be occupied by furniture with many new possibilities.

If one of the species can take advantage of a new habitat niche that is not currently occupied then it has more resources for survival and reproduction than previously, giving it an advantage.

So now you are leaving species aside and talking about a "habitat [empty] niche". I'm guessing this habitat is more where you intend your focus. A habitat niche I can understand, as it would relate to how an organism/species relates to its environment. In that sense, EVERY species has its own niche. But a void/empty niche is an empty set, being either 1) how an existing species does not relate to it's environment (nonsensical) or 2) a non-existing species interacting in an environment, which is not possible. In other words, a void/empty niche in a habitat isn't a thing.

A chair moving into the empty room has expanded the niche for chairs, and this provides opportunities for evolution. Without competition from other furniture species it can reproduce and evolve much faster than in the previous place in the habitat/ecosystem.

Thus when a massive extinction event wiped out most of the species of foraminifera, there was a void that allowed the remaining species to evolve and inhabit the niches that had been previously occupied with newly evolved species. This is what the fossil record in fact shows:

quote:
The Foram Fossils
A Classic Tale of Transition

Since the foram record extends through a major extinction event (some of the samples date back nearly 100 million years), it represents the first, grand template against which a flock of pet theories on the beginnings of evolution may now be effectively measured, he said.

Some scientists have theorized, but never been able to demonstrate, that in the absence of competition, an explosion of life takes place. The evolution of new species is greatly accelerated, and a profusion of body shapes and sizes bursts across the horizon, filling up vacant spaces like weeds overtaking a pristine lawn. An array of new forms fan out into these limited niches, where crowding soon forces most of the new forms to spin out into oblivion, as sparks from a flame.

As revealed by the ancient record left by the foram family, the story of recovery after extinction is every bit as busy and colorful as some scientists have long suspected.

"What we've found suggests that the rate of speciation increases dramatically in a biological vacuum," Parker said. "After the Cretaceous extinction, the few surviving foram species began rapidly propagating into new species, and for the first time we're able to see just how this happens, and how fast."


A profusion of new foramin species as they fill the room left by the extinction event.

... In all, there is not much here that is really a noteworthy example of evolution in a Neo-Darwinian sense. There talking about forams the whole way through, with changes that I would just consider normal diversification (like the many dog breeds, or even humans). Either way, it's the type of evolution that is no problem and even the most ardent critics of Darwinism would accept. ...

They would not have included any new species not a foramin in their study, but this is still typical creationist type comment, ignoring the point made.

Similarly, the Cambrian "explosion" of new species types that first evolve protective shells occurred because the niche for species with protective shells was empty.

Please! Evolution occurred because it saw a potential opening niche? With no explanation for the new information needed to build the new body forms and organ types, and no precursors evident?

quote:
From Message 14: ... but also that evolution would occur rapidly when there was a void in habitat that could be occupied; selection would be diminished and more varieties would survive and evolve. What that new habitat was, occurred when the ocean pH changed (due to oxygen being produced by algae iirc) and it became possible to make calcite shells. The Cambrian fossils are almost all shelled creatures, the pre-Cambrian fossils do not have shells. Having shells provides an obvious survival advantage, and those that had shells had an open habitat to inhabit: rapid evolution. Standard. Darwinian.

Evolution occurred because it became possible to make shells, and the first species to do so had an advantage over species without shells.

The same would hold for the first species on land.

Let's start with this definition of evolution as a process:

The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities for growth, development, survival and reproductive success in changing or different habitats.

About as vague and broad a definition as you could get. Basically: things change. Ok. I agree. This "evolution" happens.....
But it's missing the details regarding some proposed changes/differences between organisms in life. How and why specifically? ...

Why should that be necessary to include? "changes in the composition of hereditary traits" means traits change over generations.

... No mention of where the information required for developing major differences comes from, nor how to explain getting around the apparent limits of adaptation within species?

Information is not a thing in biology. You need to define it and have a means to measure it before it could be useful, if then.

What is a "major difference" -- the difference between species is major enough to isolate breeding.

What are "apparent limits of adaptation within species?" Curiously I am not aware of any.

Enjoy


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Dr Adequate
Member
Posts: 16104
Joined: 07-20-2006


Message 53 of 60 (862107)
08-31-2019 9:56 PM
Reply to: Message 29 by Faith
08-27-2019 7:02 PM


Christ, Faith, are you still being wrong about this?

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Faith
Member
Posts: 32950
From: Nevada, USA
Joined: 10-06-2001
Member Rating: 1.1


Message 54 of 60 (862108)
08-31-2019 10:38 PM
Reply to: Message 53 by Dr Adequate
08-31-2019 9:56 PM


Not that you've ever proved.

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WookieeB
Member
Posts: 82
Joined: 01-18-2019


Message 55 of 60 (863087)
09-19-2019 6:35 PM
Reply to: Message 48 by RAZD
08-30-2019 11:05 AM


Re: more filling in the blanks.
Wookieeb writes:

First off, pretty much nobody (that I know of) says that speciation is impossible, or never happens. ...

RAZD writes:

ummmm ... the whole point of the video was to show through math that it was virtually impossible, therefore intelligent (eg god) design.

No. You seem to have a problem with context. Or you really have failed to watch the video and read the essay by Gelernter.

First, the title of the video is "Mathematical Challenges to Darwin's Theory of Evolution". It is not 'Mathematical Challenges to speciation'. You do not seem to be able to make a distinction. You are apparently stuck on being able to define a species (as the rest of your post indicates), but then you are critiquing the video on whatever seems to be the most restrictive version against it.

Secondly, "therefore intelligent (eg god) design" is not the end point of the video either. Again, if you were paying attention, you would realize that Gelernter doesn't subscribe to ID, and Berlinsky is rather neutral and ambivalent about it. Only one of the three in the video subscribes to that stance, and it hardly was the objective of the video.

RAZD writes:

Biologists recognize that speciation is muddy,....

I agree. But if you're going to criticize the video, then you need to use the meaning that is represented in the video. Anything else is just an equivocation on your part.

WookieeB writes:

The Neo-Darwinian process is what Gelernter was referring to in the phrase you quoted. So I do not agree with you that his statement was "misinformation" or incorrect. Of course, if you want to quibble about definitions, we can. But from the context it is pretty clear on what Gelernter was referring, since he even made a differentiation between what he called "the small adjustments by which an organism adapts to local circumstances" or "the fine-tuning of existing species" with "the origin of species" (which would all fall under your definition of Evolution", vs how a Darwinian process can explain the differences. He's making a distinction that you haven't really acknowledged yet.

RAZD writes:

This type of "distinction" is also typical creationist/IDologist semantic misdirection -- which is why it is misinformation. Anytime you see the words "Darwinian" or "Neo-Darwinian" you can be pretty sure that the author is equivocating between a vary narrow view of some evolutionary processes and the full band-width of all known evolutionary processes. Pretending/implying they are the same means making the "part for the whole" logical fallacy.


Male cow feces poppycock! You're the one that is equivocating. They are pretty clear in the video on what they mean , but because you can't deal with their definitions and instead point to a different meaning, you go and call foul? Please!!!

The FIRST topic the moderator asks in the video is on definitions. After referring to a statement in the essay where Gelernter commented on what Darwin could explain in relation to small changes vs big ones, is: "Start by convincing me, ..., that you are not just defining the term "species" to Darwin's disadvantage". Gelernters response:

quote:
There really is very little disagreement on the issue of what a species is and I think it doesn't have to be a technical term. I think virtually any alert child knows when he passes from one species of pet creature to another species or, what do [you have], a cat, a cow or a sheep or something like that, this is part of our innate view of the universe. Nobody wants to define anything to Darwin's disadvantage."

I would obviously disagree with him that there is little disagreement on what a species is, or the need (in your case) to provide a technical term. But from the essay and the video, and even from what Darwin meant in his "Origin of the Species", it is clear we're talking about creatures that are very different in form and type - probably minimally on the taxonomic level of Genus or Family. And since they are also referencing animals from the Cambrian Explosion, with animals with new body plans suddenly appearing, it should be clear the distinctions they are talking about. And as for the method of changes, they are clearly dealing with Darwinian/Neo-Darwinian processes. There is no misdirection or misinformation at all.

If you don't want to or can't deal with talking about Darwinian processes, that is your problem. If you think there are some other things in the "all known evolutionary processes" wheelhouse to explain things, then you have to specify it. The essay and video has been clear on what they are talking about. You have not.

And this criticism doesn't address:
Message 19 writes:...

which standard of speciation was:
message 19 writes:

Over the last few decades the theoretically preeminent species definition has been the biological species concept (BSC). This concept defines a species as a reproductive community.


which is reproductive isolation. If that is the standard, then the items in your list, 5.2-5.8 are not examples of speciation because they are not examples of reproductive isolation.

My point is your list doesn't fulfill it's claims based on its own standards.

Thus....

The point is that biologists have recognized speciation in a multitude of instances.

... might be a true statement, but you haven't demonstrated this yet with the exception of a few plants. Which is why I said:

All the other examples in your list I would not consider speciation, since the reproductive isolation has not been established in those examples.

Again, I think that speciation can occur, depending on your definition. But by the examples given so far, even when it does, the results are trivial at best and do not demonstrate much of anything to crow about. They certainly do nothing to demonstrate or explain the origin of large-scale biological change. And some BIOLOGISTS agree with me:

quote:
Theodosius Dobzhansky:
"Reproductive isolation evidently can arise with little or no morphological differentiation."

"we are in a situation today similar to that experienced by Darwin more than a century ago: differentiation of species is inferred from copious indirect evidence, but has not actually been observed.”


quote:
Lynn Margulis and Dorion Sagan:
"Speciation, whether in the remote Galápagos, in the laboratory cages of the drosophilosophers, or in the crowded sediments of the paleontologists, still has never been directly traced.”

quote:
University of Bristol bacteriologist - Alan H. Linton:
"None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of twenty to thirty minutes, and populations achieved after eighteen hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another. . . . Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic [e.g., bacterial] to eukaryotic [e.g., plant and animal] cells, let alone throughout the whole array of higher multicellular organisms"

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WookieeB
Member
Posts: 82
Joined: 01-18-2019


Message 56 of 60 (863089)
09-19-2019 7:04 PM
Reply to: Message 49 by Taq
08-30-2019 12:59 PM


Re: more filling in the blanks.
It is fabricated because it hasn't been empirically tested. It is a fabrication of the assumptions Axe makes.

No, the results were determined via empirical testing. Experiments were done.

Now if you are saying that nobody has done 10^77 tests to determine the number, that would be true. But doing that many tests isn't the point. the 10^77 was inferred based on empirical results, and it has always just been called an estimate.

....we can see if any of those antibodies have B-lactamase activity, the function that Axe says can only occur once in every 1x10^77 combinations.

But that was not his claim. You are not properly understanding (or are just arguing a strawman) to what Axe was claiming. So your statement ends up being irrelevant.

In a library of 2 x 10^9 random peptides they were able to find 5 of those random peptides that had B-lactamase activity, well below the number given by Axe. Even if we look past all of the problems with Axe's mathematical model, reality shows us that Axe is wrong by many orders of magnitude.

Again, you are failing to understand what Axe was saying. His claim was NOT saying that finding peptides that have B-lactamase activity is 1 in 10^77. Besides, in your statement, "random" is a bit misleading, because the experiment did not use wholly "random" peptides. They were constrained in the same protein family. Nonetheless, that has little relation to Axe's claim.

You don't like Axe? Then how about other experiments that provide a roughly comparable conclusion.

Reidhaar-Olson and Sauer 1990 (Functionally acceptable substitutions in two alpha-helical regions of lambda repressor) - 1 x 10^63 sequences yielded a functional repressor fold

Yockey 1977 (A calculation of the probability of spontaneous biogenesis by information theory) - likelyhood of functional cytochrome c sequence is 10^65

Hayashi et al. 2006 (Experimental Rugged Fitness Landscape in Protein Sequence Space) - Getting the wild-type function of the g3p minor coat protein of the fd phage takes rougly 10^70 trials.


This message is a reply to:
 Message 49 by Taq, posted 08-30-2019 12:59 PM Taq has responded

Replies to this message:
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WookieeB
Member
Posts: 82
Joined: 01-18-2019


Message 57 of 60 (863090)
09-19-2019 7:08 PM
Reply to: Message 50 by RAZD
08-30-2019 1:16 PM


Re: probabilities and possibilities
My point being that you must know all the possibilities before you can estimate the possibilities. If you assume a limited number of possibilities and your model fails to reflect reality, then reality is not the problem -- the model is the problem, the assumption/s in the model are the problem.

For my die answer, within your parameters, I acknowledge my answer was limited. I was assuming the standard 6-sided die in a pair.

But I'm failing to see your bigger point. You seem to claim there is a problem with the model with regards to the math spoken of in the video and essay, but you haven't specified what that problem is. So, state your parameters that indicated an incorrect model.


This message is a reply to:
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RAZD
Member
Posts: 20120
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


(3)
Message 58 of 60 (863107)
09-20-2019 9:53 AM
Reply to: Message 57 by WookieeB
09-19-2019 7:08 PM


Re: probabilities and possibilities
For my die answer, within your parameters, I acknowledge my answer was limited. I was assuming the standard 6-sided die in a pair.

But I'm failing to see your bigger point. ...

The bigger point is quite simple: when you make (mistaken) assumptions about the possibilities your are limiting your answers to a (mistaken) subset of actual probabilities. Those assumptions should be part of the answer.

For instance you could have said: "1/6 if the dice are perfect homogeneous cubes numbered 1 to 6 on the faces."

... You seem to claim there is a problem with the model with regards to the math spoken of in the video and essay, but you haven't specified what that problem is. So, state your parameters that indicated an incorrect model.

There are only 4 numbers discussed in the video (a remarkable paucity for a "Mathematical Challenges to Darwin's Theory of Evolution" don't you think?): the number of amino acids (20), the number of possible working proteins (1 in 10^77 will result in a functional fold), the possibility of getting a "right" 150 amino acid "string of beads" (20^150 = 1.4 x 10^195), and the number of atoms in the universe (number not given, just the comment that it is less than 20^150 = 1.4 x 10^195).

This should be a big red flag.

They are all (except for the number of amino acids used), WAG (wild ass guess) assumptions, bald assertions or outright falsehoods.

There is no mathematical proof.

As I've already shown in Message 51, the 20^150 = 1.4 x 10^195 calculation is wrong, badly, grossly wrong, because it only uses one of the worst possible ways to assemble 150 amino acids, one by one in order.

Question for you: why was a 150 amino acid string protein chosen?

Consider that the first life would be the simplest, using the simplest molecules. As noted in Message 51 the smallest known protein is made with only 20 amino acids.

Why choose a much more complex protein than necessary if the argument is that it's formation has a low probability?

Enjoy


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RAZD
Member
Posts: 20120
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.8


(3)
Message 59 of 60 (863116)
09-20-2019 11:32 AM
Reply to: Message 55 by WookieeB
09-19-2019 6:35 PM


Re: more filling in the blanks.
Wookieeb writes:

First off, pretty much nobody (that I know of) says that speciation is impossible, or never happens. ...

RAZD writes:

ummmm ... the whole point of the video was to show through math that it was virtually impossible, therefore intelligent (eg god) design.

No. You seem to have a problem with context. Or you really have failed to watch the video and read the essay by Gelernter.

Okay, let's say they are talking about major change instead of speciation. Whatever "major change" means, because it is irrelevant to biology. Biology develops changes via speciation -- becoming different species, then evolving separately, diverging, adding change to previous changes.

RAZD writes:

Biologists recognize that speciation is muddy,....

I agree. But if you're going to criticize the video, then you need to use the meaning that is represented in the video. Anything else is just an equivocation on your part.

(1) so they are talking about speciation?

(2) nope. I need to use what actual biologists use. Anything else would be spreading misinformation.

message 19 writes:

Over the last few decades the theoretically preeminent species definition has been the biological species concept (BSC). This concept defines a species as a reproductive community.


which is reproductive isolation. ...

Not necessarily. A reproductive community is composed of the individuals that happen to reproduce, as opposed to all the individuals that are capable of reproduction. This definition actually works better for single cell organisms.

Consider horses and donkeys. They -- to use the rather childish definition in the video -- are readily recognized as different species, yet they can interbreed.

... If that is the standard, then the items in your list, 5.2-5.8 are not examples of speciation because they are not examples of reproductive isolation.

My point is your list doesn't fulfill it's claims based on its own standards.

Curiously I see biologists handing out new species names, and I trust them more than non-biologists.

Which is why I said:
All the other examples in your list I would not consider speciation, since the reproductive isolation has not been established in those examples.

You are the one changing the definition used on the list.

Again, I think that speciation can occur, depending on your definition. But by the examples given so far, even when it does, the results are trivial at best and do not demonstrate much of anything to crow about. ...

Speciation is an opportunity for divergence in evolutionary paths for reproductive communitites, breeding populations. That divergence is manifest in change, increasing differences between daughter populations.

... They certainly do nothing to demonstrate or explain the origin of large-scale biological change. ...

And now we come to the crux. What is "large-scale biological change?" A new species?

... And some BIOLOGISTS agree with me:

Whoopie, there is disagreement. I also smell quote mining. This ...

quote:
Theodosius Dobzhansky:
"Reproductive isolation evidently can arise with little or no morphological differentiation."

"we are in a situation today similar to that experienced by Darwin more than a century ago: differentiation of species is inferred from copious indirect evidence, but has not actually been observed.”


... appears to be more about cryptic species evolution than evolution in general.

Care to provide actual references to those quotes citing the authors actual works?

Enjoy

Edited by RAZD, : .


we are limited in our ability to understand
by our ability to understand
Rebel•American•Zen•Deist
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 Message 55 by WookieeB, posted 09-19-2019 6:35 PM WookieeB has not yet responded

  
Taq
Member
Posts: 8012
Joined: 03-06-2009
Member Rating: 4.6


(2)
Message 60 of 60 (863125)
09-20-2019 1:20 PM
Reply to: Message 56 by WookieeB
09-19-2019 7:04 PM


Re: more filling in the blanks.
WookieeB writes:

No, the results were determined via empirical testing. Experiments were done.

The conclusions Axe drew from the results were faulty and fabricated. He assumed that his experiment would capture all possible B-lactamase proteins.

But that was not his claim. You are not properly understanding (or are just arguing a strawman) to what Axe was claiming. So your statement ends up being irrelevant.

If Axe's claim is not relevant to the chances of a functional B-lactamase emerging from random sequence, then his claim is irrelevant to evolution.

His claim was NOT saying that finding peptides that have B-lactamase activity is 1 in 10^77.

Then what is it?

Besides, in your statement, "random" is a bit misleading, because the experiment did not use wholly "random" peptides. They were constrained in the same protein family.

So you are saying that it is easy to evolve a B-lactamase enzyme by randomly changing a small portion of the same protein? If so, then what is your problem with evolution?


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