What does “molecular crowding” (the fact that a cell’s cytoplasm …

Comment on The Basis of Biblical Credibility by Sean Pitman.

What does “molecular crowding” (the fact that a cell’s cytoplasm is densely packed with all kinds of molecules) have to do with the concept of discovering new types of beneficial proteins within “sequence space” at various levels of functional complexity? You do realize that sequence space is the space that contains all possible protein sequences of a given length? – and that sequence space has absolutely nothing to do with “molecular crowding”? In other words, the fact of molecular crowding doesn’t make it any easier to find the rare islands of novel beneficial sequences within the vast ocean of sequence space via random mutations.

For example, what is the sequence space size for sequence length of 100aa? It is 20^100 or 1e130 sequences. This is a larger number than all the atoms in the visible universe (~1e80 atoms). Clearly, the concept of “molecular crowding” has nothing to do with the concept of sequence space, which is an entirely different concept. The question is, what is the ratio of potentially beneficial vs. non-beneficial sequences within sequence space? In other words, how many random mutations would it take, on average, to an existing sequence within a genome to get it to mutate into another kind of beneficial sequence? That’s the real question.

Here’s a big clue for you: The density of potentially beneficial sequences within sequence space is very low, even at low levels of functional complexity. It is not “crowded” at all – not even close. There are always more non-beneficial sequences compared to potentially beneficial sequences in sequence space. And, it gets exponentially less and less crowded (with potentially beneficial sequences) with each step up ladder of functional complexity (i.e., with each increase in the minimum size and/or specificity requirements under consideration). This means, of course, that it is exponentially harder and harder to find, within a given span of time, novel islands of beneficial sequences within sequence space at higher and higher levels of functional complexity.

Should you really be regarding him as your oracle? Shouldn’t you like the Bereans look at the literature to see if what he says is so?

By all means everyone who is at all interested in the implications of these concepts should research the arguments carefully to see who is telling the truth here. Personal research is vital to know if what the “experts” are saying about Darwinism, specially regarding the creative ability of random mutations and natural selection, actually hold water… or even if someone like Dr. Paul Cameron even understands basic concepts like “sequence space” and how random mutations must randomly search through many junk sequences in sequence space before natural selection can do anything…

Sean Pitman
www.DetectingDesign.com

Sean Pitman Also Commented

The Basis of Biblical Credibility

Your argument that evolution cannot work because Paul Cameron or anyone else lacks a precise mechanism to overcome your declared barrier (1000 fairly specified amino acid residues) is based on the fallacy of ignorance.

Then I suppose SETI science, forensic science, and anthropology are all based on the “fallacy of ignorance” as well? – since these scientists can’t think of any mindless natural mechanism to explain certain types of radio signals, murder victims with certain unnatural features, or pieces of rock with artefactual features?

I’m sorry, but there is no fallacy with the argument for the detection of intelligent design behind various kinds of artefacts – like the origin of a highly symmetrical polished granite cube. It isn’t that these scientists are ignorant of how the phenomenon in question could have been produced by intelligent design. They know how the features they’re considering could have been produced by many different intelligently designed methods. What they don’t know is how the artefact in question could have been produced by any known mindless mechanism of nature. That, my friend, is the very basis of all sciences dealing with the detection of true artefacts of intelligent design.

The very same thing is true of the biomachines within living things that I’m presenting. Clearly, these machines very closely resemble machines that we know were produced by intelligent design. We known and understand how such machines could be produced by various means by intelligent design. What we don’t know is how they could be produced by any mindless natural mechanism this side of a practical eternity of time (i.e., trillions upon trillions of years). This means, of course, that the very best scientific conclusion, the theory with the best predictive power, is that any such biomachine was almost certainly produced by intelligent design.

Now, does the intelligent designer of these biomachines have to be God? No. Not at all. Omnipotence is not required to explain something like a bacterial flagellar motility system. However, even though omnipotence is not required to explain the origin of such machines (to include things like a wrist watch or a granite cube), intelligence of some kind is required.

Does this therefore mean that God did not make something just because God-like power is not required? No. God can make simple stuff just as easily as you and I can make simple stuff. If it just that a God-like creative power is not required to explain everything that God can make. For example, is it possible for God to make a loaf of bread? – the same type of loaf of bread that your mother can make? Sure it is.

It’s funny, don’t you think, that you don’t argue against SETI radio signals or highly symmetrical granite cubes as being anything other than obvious artefacts of intelligent design. Why then the double standard for biological machines that are even farther beyond any known mindless mechanism while being at least closely approximated the creative powers of known intelligent agents?

Sean Pitman
www.DetectingDesign.com


The Basis of Biblical Credibility

You obviously can declare anything you want in terms mutation rates and how many SNP indels and genes were present in the 2 mythical pigs but how many can really be present in the original haplotypes. You have said before that copy number variation was not at all the basis for the genetic richness of the original 2.

I see no reason to argue for a significant difference in past mutation rates as compared to today’s rates. Consider that the pig genome is similar in size to the human genome, ~3 billion bases (haploid). The two pigs on the Ark could easily have had a 0.3% difference in genome sequences to start with (with regard to SNPs). Also, in each family line novel SNPs are produced in each generation for each individual at a fairly high rate (up to 100 per individual per generation). And, the generation time for pigs is ~1 year. A comparison between hundreds of pigs from different family lines, even within the same breeding population of average size, would yield a huge number of SNPs in very short order. So, I don’t see why this is an appeal to “magic”?

As far as “unique genes” are concerned, much of this can be explained by a loss of genetic information by one population vs. the other after the split. This is one of the reasons for the “hybrid vitality” already mentioned. Producing such hybrids gives the hybrid offspring access to genes that are missing from each separate gene pool, but were originally available in the ancestral gene pool.

Of course, the production of novel alleles is also a factor. And, in an average population, any beneficial allelic variation would become fixed in relatively short order.

The differences in indels is interesting, but I see no need to invoke magic to explain a few hundred thousand indels in a comparison of hundreds of pigs – especially since muticharacter mutations are quite common as well and would already have existed within the first pair on the Ark to begin with. For example, there are thought to be thousands of conversion mutations per individual in each generation. Combine this with what is generally assumed to be a high rate of inversions/translocations, ~10 duplications/insertions/deletions (changing up to 20 times the number bases that point mutations change per generation), and >100 satellite mutations, and you have yourself a very high overall mutation rate that adds up to many thousands of nucleotide changes per individual per generation.


The Basis of Biblical Credibility

“The discovery of the Cit + mutants in Lenski’s experiment has been a mote in the eye for those suggesting that major phenotypic innovations cannot be explained by micro-evolutionary (gradual) processes…

Do you know anything about the experiment where Lenski’s produced Cit+ E. coli bacteria?

What Lenski did was to grow E. coli under oxic conditions in citrate-rich media. E. coli bacteria are generally unable to use citrate under oxic conditions as a source of energy. However, they can use it under anoxic conditions. In other words, they already have the gene for citrase in their genome. It is just that it is normally turned off under oxic conditions. How is it turned off? Well, the promoter for the gene that transports citrate into the bacterium is not active under oxic conditions. So, all that needs to happen is to move the citrate transport gene close to a promoter that is actually active under oxic conditions. Once this is done, citrate will enter the bacterium and be used for energy.

And, this is exactly what happened. Nothing structurally new needed to be evolved. After about 31,000 generations, in a large population of bacteria, there was a single genetic mutation in a bacterium that ended up moving the citT gene and placing it under the control of a promoter (rnk) that is active under oxic conditions. The fact that just this single translocation mutation took so long to achieve should clue you in to how difficult it is to achieve even such low-level changes in function via random mutations. The protein product, however, remained the same – i.e., <500aa with no required amino acid changes to achieve a selectable effect. All that was required was to move a pre-existing gene close to a promoter to turn it on during oxic conditions. That's it. The protein itself didn't need to be changed for a useful advantage. Now, at this point, multiple copies of the gene were rapidly produced in some colonies. However, having just one copy was enough to produce a selectable advantage in the citrate-rich environment. It doesn't matter if there are 1 - 9 copies of the gene - the same function is realized to different levels - i.e., the cit+ function can exist, to a selectable degree, with just one copy of the gene producing the the very same protein. Additional "refinements" are easy once at least a minimum useful level of a particular type of function is realized - not a problem at all. Again, this "unicorn" of yours is a very low-level example of evolution in action where nothing structurally new was produced to achieve the function in question. The only thing that happened was a mutational move from one location to another within the genome. That's not a statistical problem for Darwinism at all...

Pubmed still does not have any reference to novel structure composed of 1000 amino acid residues. But indeed there is refence to uinicorns so your 100FSAAR is rarer than unicorns in the biomedical literature. Perhaps you should publish your obvservations.

Tell me, what is the minimum number of specifically arranged amino acids required to produce a rotary bacterial falgellar motility system? Is it possible to reduce it to less than 1000 specifically arranged residues? – without a complete loss of the motility function?

Again, the concept of functional complexity has been published and is well defined in literature, to include the minimum size requirement. I’ve already given you the references a couple times now.

Sean Pitman
www.DetectingDesign.com


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I fail to see where you have convincingly supported your claim that the GC leadership contributed to the harm of anyone’s personal religious liberties? – given that the GC leadership does not and could not override personal religious liberties in this country, nor substantively change the outcome of those who lost their jobs over various vaccine mandates. That’s just not how it works here in this country. Religious liberties are personally derived. Again, they simply are not based on a corporate or church position, but rely solely upon individual convictions – regardless of what the church may or may not say or do.

Yet, you say, “Who cares if it is written into law”? You should care. Everyone should care. It’s a very important law in this country. The idea that the organized church could have changed vaccine mandates simply isn’t true – particularly given the nature of certain types of jobs dealing with the most vulnerable in society (such as health care workers for example).

Beyond this, the GC Leadership did, in fact, write in support of personal religious convictions on this topic – and there are GC lawyers who have and continue to write personal letters in support of personal religious convictions (even if these personal convictions are at odds with the position of the church on a given topic). Just because the GC leadership also supports the advances of modern medicine doesn’t mean that the GC leadership cannot support individual convictions at the same time. Both are possible. This is not an inconsistency.