Why I remain a Darwin Skeptic

[glipsnort (Steve Schaffner)]

In this study, a library of 6x10^12 random proteins yielded four proteins with a single function, ATP binding. Since the number of possible functions is very large, this is an extremely conservative estimate of the fraction of all proteins that are functional.

[T_aquaticus]

@Relates

No one doubts except perhaps Dawkins that ecology is a science.

Huh?

Dawkins has sat on judging panels for awards as diverse as the Royal Society’s Faraday Award and the British Academy Television Awards,[44] and has been president of the Biological Sciences section of the British Association for the Advancement of Science. In 2004, Balliol College, Oxford, instituted the Dawkins Prize, awarded for “outstanding research into the ecology and behaviour of animals whose welfare and survival may be endangered by human activities”.[55] In September 2008, he retired from his professorship, announcing plans to “write a book aimed at youngsters in which he will warn them against believing in ‘anti-scientific’ fairytales.”[56]

The Dawkins Prize is awarded to outstanding research in the field of ecology.

[T_aquaticus]

@Daniel_Fisher

As anticipated…

To add to what @glipsnort said, a protein with beta-lactamase activity was found in a random antibody library of 2.7x10^9 sequences.

Multitarget selection of catalytic antibodies with β-lactamase activity using...

Some ID proponents want to claim that it would tak 10^64 or some crazy number in order to find lactamase activity, but in the real world it takes just 10^9.

[Relates (Roger A. Sawtelle)]

@Shekar

II) Depending on how you think about ‘random’, something like transposable elements allows for adaptation in response to environmental conditions.

I agree with you about ecological natural selectio0n, but “science” as @Klax points out has not accepted it, nor has BioLogos. Do you stand with me against survival of the fittest is not scientifically verified?

@Shekar, thank you for the article on Endosymbiosis. It clams to say that symbiosis does not play a leading role in evolution, BUT 1) I read that Margulis rejects the false dualism of cooperation and competition, while I do not find this in Survival of the fittest. For instance Symbiosis includes some competition in predation, 2) the article itself was about the role of symbiosis in genetic change and says that it does play an important role, but not a dominant role. 3) the article fails to discuss the role of symbiosis in Natural Selection which is where it is most important and dominant in my experience and study.

In my view the article continue4s that strange myopia which seems to keep evolutionists from evaluating how and why Natural Selection works and the role that symbiosis plays in it.

@sfmatheson

: there’s no such discipline as “ecological evolution.”

True, and there is also no such discipline as Evolutionary Creation or even Natural Selection. Ecological evolution or ecological natural selection is a term which describes an understanding of how evolution takes place. It is scientific because it is based on scientific research. If you disagree with it, you are free to offer a different scientific view.

[T_aquaticus]

@Daniel_Fisher

The whole system is more brilliant than anything I had ever come up with. It struck me that if mankind were given the task, given only what we know about molecular/organic chemsitry, to come up with a system that could keep a database of 1000 proteins and be able to transcribe and “print” them… it would prove an impossible task for us. Then the line I’d heard about somehow organic matter getting zapped by electricity or thermal vents or sunlight, then just somehow getting formed into these processes began to move for me into the realm of high fantasy.

First off, scientists aren’t that impressed by arguments from incredulity. Human intuition is often wrong which is why we came up with the scientific method to begin with. Just because you find it impossible does not mean reality is prevented from doing it.

Second, how do you think life came about, and would that classify as high fantasy?

@Daniel_Fisher

For the system to work, you needed DNA. You needed RNA (and the process by which it gets copied). You needed a coordinated/coded system somehow for the tRNA to latch onto very, very specific amino acids (and only those) for the entire system to work; and then you need a very, very, very, very specifically shaped and designed ribosome in order to make the system work. You needed ALL of these to get anything. This is years before Behe’s first book, but I recognized what came to be known as “irreducable complexity.”

We would need some evidence to back up these claims. What you describe is true for modern life, but it may not hold for the first life.

@Daniel_Fisher

Finally, what in my background started to increase my skepticism… one of my professors had done significant work with mutations and shared with us that he considered it impossible that mutations could have much to do with evolution - now he was an absolute Darwin devotee, but he shared that in all his work and knowledge, mutations just don’t do what is necessary.

“Darwin devotee” gives away your bias. It’s just evolution, and scientists are just scientists, not devotees.

If this supposed professor thinks mutations don’t have much to do with evolution then how in the world does this professor explain the physical differences between species? The only explanation I can come up with is differences in the DNA sequence of the genomes, which are mutations. Humans and chimps are different from each other because of the mutations that separate us. Every person is different from every other person because of mutations. The reason alleles exist is because mutations happen.

I would strongly suggest that you read @glipsnort’s article on mutations, and how there is mountains of evidence supporting the conclusion that the differences between species is due to mutations:

https://biologos.org/articles/testing-common-ancestry-its-all-about-the-mutations

@Daniel_Fisher

It didn’t take me long to realize, though, that population genetics have an effect on changing what already exists in the genes, but it isn’t going to “invent” something new.

How did you come to this conclusion?

[T_aquaticus]

@Daniel_Fisher

So to be generous, I speculated that perhaps there are 100 quintillion (100,000,000,000,000,000,000) possible combinations that would allow a certain biological function (some more effective than others, of course.)

That would be speculation, not an assumption. It is also an incorrect speculation. For example, there are 10^93 possible combinations that can produce cytochrome c as we know it:

Importantly, Hubert Yockey has done a careful study in which he calculated that there are a minimum of 2.3 x 10^93 possible functional cytochrome c protein sequences, based on these genetic mutational analyses (Hampsey et al . 1986; Hampsey et al . 1988; Yockey 1992, Ch. 6, p. 254).
29+ Evidences for Macroevolution: Part 4

Those calculations are just for the fitness peak that cytochrome c currently sits on. There could be other fitness peaks out there for that same function.

@Daniel_Fisher

I noticed, for instance, that it is believed that in a (mere) 10 million years, or 1 million generations (given ~10 year generation time in dolphins and whales), echolocation developed in whales/cetacea, along with a new specialized organ to aid that process. But if I expressed skepticism about that, that we don’t observe such complexity forming in this process, I was always told that it is just too slow for us to see. We can’t observe a million generations of whales. It occured to me, “Why not look for an analogous process in a species we can observe for over a million generations?” and it occured to me, since the invention of microscopes capable of observing bacteria, we have been able to observe and document organisms like e coli over the last 50 years or so. In ideal conditions they can reproduce every 20 minutes or so. In the most ideal conditions, that is around 25,000 generations in a year, which would allow potentially somewhere close to a million generations across billions upon billions of organisms in 40-60 years. Again, people can challenge specific assumptions, but the basic observation doesn’t change:

Bacterial genomes can not be a model for vertebrate genomes. The size and gene count are very different. Gene interactions are very different. If you are really looking for a realistic model for bacteria then you need to let bacteria multiply for about 2+ billion years because that is how long it took for multicellular life to emerge from single celled life in Earth’s history.

@Daniel_Fisher

ENGINEERING PRINCIPLES - Now, if I haven’t said it earlier, I have no difficulty whatsoever with the basic principles of what is called microevolution. but even in the engineering world, there are “improvements” to basic systems, where the basic system remains intact, and we continually make new upgrades, and radical overhauls that simply can’t be done by a series of minor adjustments. The propeller driven P51 planes of WWII could theoretically be traced out as the “ancestors” of our modern turboprop planes, more or less. A slight increase in propeller speed here, a fatter wing there, etc., one can appreciate how a series of slight changes can make basic improvements to a system (or better adapt it to other environments), while the essential system remains the same. Modified bird beaks, etc.

Compare the chimp and human genomes and determine which specific differences are microevolution and which are macroevolution. Which point mutations are macro and which are micro?

@Daniel_Fisher

Transforming a regular flight bird into a hummingbird would be comparable - a hummingbird’s design is so ridiculously precise, integrated in so many parts (neurological, wing structure, digestion, instinct, etc). to allow it to hover with such precision or flap wings with that kind of speed. Everything about it suggests to me it is not the kind of endstate that could be achieved by a series of random variations, however assisted by natural selection.

I don’t doubt that it seems that way to you, but that’s not how science works. In science, we need evidence, not subjective opinions.

[T_aquaticus]

@Daniel_Fisher

Finally (last point for now I promise)… people talk about “how similar” human DNA is to that of chimpanzees. Only a 2% difference, I understand. Sounded impressive to me, again, until I started doing the math… 2% of 3,000,000,000 (base pairs) is 60,000,000 differences in our DNA. Doesn’t seem quite as small to me when it is stated that way. Wikipedia tells me we have around 64 mutations per generation. HCLCA and humans diverged maybe some ~700,000 generations ago or so. Getting all the right mutations to make us what we are seems very , very fortuitous.

Let’s do the math.

Each human is born with about 50 point mutations, and about 25 years for each generation. In a constant population of just 100,000 humans that would be 200,000 mutations per year in this model population. If humans diverged from the chimp lineage 5 million years ago that would be 1x10^12 mutations total that did happen in the human lineage. The human diploid genome is only 6 billion bases, so that’s enough mutations to change every base in the human genome more than 100 times. In fact, it only takes 180 million births (on average) to get all possible point mutations in the current human genome.

We are separated from chimps by about 40 million mutations. Let’s say half of those mutations happened in the human lineage, so about 20 million, or 2x10^7. This means that for every 50,000 mutations we only needed to keep 1 in order to get humans from a common ancestor shared with chimps.

You also state that they had to be the “right” ones. That’s false. You are drawing the bulls eye around the arrow. Chimps didn’t get the same mutations we did, and they still evolved. There is no such thing as the “right” mutations in evolution, only the ones that do happen and the ones that are selected for. Paraphrasing Stephen Jay Gould, if we rewound the tape of evolution and let it play again we wouldn’t expect the same result.

[Daniel_Fisher]

@T_aquaticus

First off, scientists aren’t that impressed by arguments from incredulity.

Well, to be clear, I am responding to @Shekar’s specific question about why I am and remain incredulous. I’m not making a positive argument here. This is my own personal testimony. You’re welcome to critique my facts and interpretations, of course, and demonstrate to me where I’m missing something, That would be most welcomed… but let’s use the appropriate criteria. I’m not making a positive argument to convince someone else, I’m explaining my own personal skepticism.

@T_aquaticus

To add to what @glipsnort said, a protein with beta-lactamase activity was found in a random antibody library of 2.7x10^9 sequences.

This could be very relevant data indeed. One question to clarify… was the library of 2.7x10^9 that you reference a library of random amino acid sequences, or a library of already confirmed, documented/recorded, functional proteins (antibodies)? This would be of great significance to my core question.

[T_aquaticus]

@Daniel_Fisher

I’m not making a positive argument to convince someone else, I’m explaining my own personal skepticism.

That is my understanding of your posts as well. What I am trying to convey is the reasons why scientists come to a different conclusion than you do. The first big difference is that scientists don’t use logical fallacies, like arguments from incredulity, to falsify scientific theories. No theory has ever been thrown out because some scientist just finds it too incredible, despite all of the evidence that supports the theory.

@Daniel_Fisher

This could be very relevant data indeed. One question to clarify… was the library of 2.7x10^9 that you reference a library of random amino acid sequences , or a library of already confirmed, documented/recorded, functional proteins (antibodies)? This would be of great significance to my core question.

Antibodies have constant regions and random regions. The random region is about 100 amino acids long, and it is produced by randomly mixing sections of a gene together. The process is called V(D)J recombination:

V(D)J recombination

The random nature of the recombination events also shifts reading frames around, so it isn’t as if it is joining sections of an existing protein together. This is all a part of B-cell maturation, and it produces your antibody library that you are born with. The variation in sequences allows different antibodies to bind to different antigens, such as those found on bacteria and viruses, or even cancer cells.

Since these are a natural random protein library, they can be used to test for different protein functions. This is exactly what the scientists did in the paper I cited. They found a random sequence from an antibody library that had lactamase activity.

[Daniel_Fisher]

Very interesting and useful indeed. Thank you for that reference, I will add that to my library. One other quick question, can you point me to the ID Proponent’s alternate claim about the odds being closer to 1 in 10^64?

[Klax (The only thing that matters is faith expressed in love.)]

@Daniel_Fisher

MATHEMATICS - The one significantly “new” thing to me was in understanding just how unlikely we are talking. I’d never done the math before reading “Signature in the Cell.” I had brushed off my creationist friend’s “just forming one protein is so unlikely” claim by the “sure, but given enough time and opportunities” hand-wave. But Meyer’s book walked through the actual math involved, and I started doing some calculations myself. For a rather small, modest length protein of say 100 amino acids, there is something like 10^130 different combinations of such. Now of course, there isn’t just one solitary single sequence (or number) that will produce a certain biological function, but then common sense with my little science background suggested they can’t be practically innumerable, either. So to be generous, I speculated that perhaps there are 100 quintillion (100,000,000,000,000,000,000) possible combinations that would allow a certain biological function (some more effective than others, of course.) And then, let’s presume an ocean full of amino acids (from many fortuitous occasions of the Miller-Uray process), where we allow a trillion times every second, across the last 10 billion years, amino acids have just been combining, searching for this particular biological function… If I did my math rightly, this rather generous process allows only a 1 in 10^90 chance of finding said functional protein. We could increase the number of “functional combinations” of amino acids by a factor of another quintillion and the difficulty would remain. In Meyer’s book I recall he put it in perspective - it is somewhere in the neighborhood of someone picking at random a single atom in the entire observable universe, and then I also blindly pick the same atom. And only one shot. People have and can critize my assumptions, but have never been able to give me hard numbers (or even ballpark ones) that would change the basic difficulty here - but this is what gave me a sense as to the ridiculously huge difficulty in getting just one fraction of these processes right, not to mention the layers upon layers of integrated complexity needed for life to work.

Evolution works forwards, not backwards. But not to any teleology.

[EricMH (Eric Holloway)]

@Daniel_Fisher

If I did my math rightly, this rather generous process allows only a 1 in 10^90 chance of finding said functional protein.

I was thinking about this as I read Dawkins’ explanation of how gene regulation works in embryology. I wonder if you are off by a few exponentiations? Not only are the correct genes required, which is a specific amino acid ordering, but the genes must also activate in the right order. Thus, we have not a single exponentiation, but a double.

On top of that, various species must coexist with mutual beneficience in the same ecosystem. So, now we have multiple gene regulatory networks that must work together, with is yet another exponentiation.

This means the search space is absolutely enormous. And by curse of dimensionality, we expect the good enough solutions to mostly be disjoint and sparse. Which means if evolution does work the search space is so atypical so as to be impossible, from a purely mathematical perspective.

As a side note, if you of an engineering mindset, you should read Dembski et al. book “Introduction to Evolutionary Informatics”. Very hands on application of Dembski’s mathematical theories to evolutionary algorithms and artificial life simulations, so you understand for yourself what concepts like CSI and conservation of information mean practically.

[T_aquaticus]

@Daniel_Fisher

One other quick question, can you point me to the ID Proponent’s alternate claim about the odds being closer to 1 in 10^64?

Sure:

An alignment of homologous domain sequences is used to deduce the pattern of hydropathic constraints along chains that form the domain fold. Starting with a weakly functional sequence carrying this signature, clusters of ten side-chains within the fold are replaced randomly, within the boundaries of the signature, and tested for function. The prevalence of low-level function in four such experiments indicates that roughly one in 10^64 signature-consistent sequences forms a working domain.
https://www.sciencedirect.com/science/article/pii/S0022283604007624

V(D)J recombination was able to do it in about 10^9 attempts.

[T_aquaticus]

@EricMH

Not only are the correct genes required, which is a specific amino acid ordering, but the genes must also activate in the right order.

You are painting the bulls eye around the arrow. Evolution is a contingent process meaning that there were multiples paths that could have been taken and the results we see are just one path out of many.

@EricMH

This means the search space is absolutely enormous. And by curse of dimensionality, we expect the good enough solutions to mostly be disjoint and sparse. Which means if evolution does work the search space is so atypical so as to be impossible, from a purely mathematical perspective.

Until you can define the space you really don’t have much of an argument.

How could you show us all possible DNA and amino acid sequences that could serve as gene promoters?

[EricMH (Eric Holloway)]

@T_aquaticus

Evolution is a contingent process meaning that there were multiples paths that could have been taken and the results we see are just one path out of many.

You should look up “combinatorial explosion”. We are looking at least threefold explosion here. If that doesn’t bother you, not much more I can say

[sfmatheson]

@EricMH

I was thinking about this as I read Dawkins’ explanation of how gene regulation works in embryology. I wonder if you are off by a few exponentiations? Not only are the correct genes required, which is a specific amino acid ordering, but the genes must also activate in the right order. Thus, we have not a single exponentiation, but a double.

This is spectacularly wrong. I’m disappointed that you haven’t tried to understand the topics that you write about. And I’m especially disappointed that you won’t stop to ask how it is that others who know far more than you do have reached different conclusions.

[T_aquaticus]

@EricMH

You should look up “combinatorial explosion”. We are looking at least threefold explosion here.

You would need to show that these all had to happen at the same time, or that they did happen at the same time.

[Relates (Roger A. Sawtelle)]

@T_aquaticus

The Dawkins Prize is awarded to outstanding research in the field of ecology.

If Lovelace and Margulis are the thinkers behind ecology, then Dawkins is anti-ecology. If Daisy World is about ecology, then Dawkins is against ecology. If the Selfish Gene is against ecology, and it is, then Richard Dawkins is against ecology.

Dawkins is a person who believes that the universe is basically Many, many molecules. Ecology and symbiosis sees the eco-world as basically One, unity, Life. They are very different, and for Dawkins that makes ecology, such as niche construction theory and the Social Conquest of Earth wrong.

[T_aquaticus]

@Relates

If Lovelace and Margulis are the thinkers behind ecology, then Dawkins is anti-ecology. If Daisy World is about ecology, then Dawkins is against ecology. If the Selfish Gene is against ecology, and it is, then Richard Dawkins is against ecology.

Disagreeing with ecologists does not mean you are anti-ecology.

@Relates

Dawkins is a person who believes that the universe is basically Many, many molecules. Ecology and symbiosis sees the eco-world as basically One, unity, Life. They are very different, and for Dawkins that makes ecology, such as niche construction theory and the Social Conquest of Earth wrong.

Can you please cite Dawkins saying niche construction is false?

[Relates (Roger A. Sawtelle)]

Dear Friends,

I think that you haver proven my statement concerning the need for a third option.

Evolution works, but it is not random variation in a Void. Natural Selection is needed, but neither Darwin nor Dawkins have provided a viable working model to make Evolution a process which is powered by anything but change, which is Not Valid. In that se3nse the argument of @Daniel_Fisher are right.

@T_aquaticus, @sfmatheson, your arguments are right as far as they so, but one cannot say that Variation produces evolution alone. Variation can produce many, many new alleles without producing new organisms, if there is no Natural Selection.

Can anyone really say that there would have been any evolution over the last 13 million years if the earth had not changed from a huge hunk o dead basalt into a planet with water in its seas and oxygen in its atmosphere? How could humans evolved if the dinosaurs has no9t died out and we had not fought through the ices age? We know that evolution is affected by the ecology. Why not just admit it?