EvC Forum: The Origin of Novelty

mindspawn writes:

Do you really think that is what they meant when they said "They already harbor latent reservoirs". The way you describe it, its as if the latent ability they referring to , is merely the ability to evolve one day. Which evolutionists claim about the whole genome. I believe they were referring to something more specific when they used the term "harbour latent reservoirs", the implication is that abilities are already in place, the design for potential change is already there.

What they are pointing out is that a lot of potential to adapt to a variety of toxic environments is there on a lot of genes. Understand the rest of the paper, and you will understand the context of "latent". What that means in terms of what we were discussing is that there is a lot of potential for advantageous duplications to take place, because they identified all these circumstances in which amplification would be advantageous. Why you got excited by the word "latent" and associated it with "design" I don't know.

mindspawn writes:

bluegenes writes:

You already know that point mutations can change the protein product of coding genes in ways that are advantageous or neutral.

You say "I already know" this. This is the subject of this thread, but I remain unconvinced. There have been one or two unconvincing examples of this essential evolutionary process, EVER observed.

Where did you get that information from? One or two!!!! In the Lenski experiment alone, there are 10 to 20 beneficial point mutations in each of the 12 cultures he has divided his original clones into, plus far higher numbers of neutral mutations that have gone to fixation in each culture.

mindspawn writes:

But never observed combined with an extra coding gene, ie DNA based novel functions are always a claimed CHANGED function, rather than new additional function.
You are welcome to re-post any such evidence if I have missed it, remember I did not participate in the early part of this thread. And the E.Coli example of aerobic functionality, I refuted by comparing it to the aerobic qualities of the staphylococcus and pointing out the already existing aerobic promoter in the E.coli, which indicates a revitalization of an existing aerobic function, rather than a novel function per se.

No, you didn't refute anything. You just misunderstood the paper. A new gene was created. See below, where you bring it up again.

mindspawn writes:

Everything has the potential to adapt according to evolutionists, therefore I think you are understating the usage of the word "latent" in that article, by relating it to general evolutionary processes, rather than specific observances of latent already existing ability in that genome. Latent ability needs a process to get there, and yet theoretically there is nothing in variation and natural selection that would be able to select for latent ability, selection acts on blatant ability, actual fitness advantages, rather than latent/potential fitness advantages. Thus specific latent ability points more towards design than evolution.

The ability to adapt is a fitness advantage. Think about it. What would prevail in an ever changing world, strains of self-replicators with the ability to adapt, or those that remained always the same?

mindspawn writes:

bluegenes writes:

You'd have noticed that there are about thirty amplifications of the new gene in the Antarctic fish paper which is mentioned in the subtitle above if you'd read it carefully. There are variations by point mutation between these, as well. They are, from memory, 97% to 99% identical. Read the paper carefully, and you will see that they have analyzed a historical sequence of events which happened entirely by common types of mutation that can be observed in the lab. There's a duplication, which enables one copy to mutate away from the primary function and form the anti-freeze protein, then further duplications of the new gene.

Kindly re-post the link, I haven't got the time to look for old links in this thread.

For the third time on this thread and the fourth time in all: Novelty by duplication, point mutation, and multiple amplifications in a fish.

You seem to have the time to contradict experts in a number of fields, including genetics, but no time to familiarize yourself with the very large amount of research information available in the fields you're criticizing. And impressively, according to your own view in one of your posts, you're managing to do all this with a brain the size of a gorilla's.

mindspawn writes:

bluegenes writes:

If you read and understand the various papers I've shown you, you should be able to see very clearly that novel protein coding genes can be produced by well established processes. Duplication, then point mutation on one or both of the copies.

No-one has EVER proved the process of duplication together with novel function. That is purely in the realm of speculation.

Not to those of us who understand the fish paper, and other similar research.

mindspawn writes:

If its shown to me that its possible in theory, there's still more processes to prove, ie does it ACTUALLY happen (I can tell you it has never been observed)

Then you don't understand observation. It doesn't have to be direct. How would you try to make the case for a world wide flood 4,500 years ago? By observing the evidence of the event which would remain in the present. How do you think murderers are convicted "beyond all reasonable doubt" in cases with no eye witnesses? The same way.

There are a number of ways that the past can be read by observing genomes in the present.

mindspawn writes:

and is it so prevalent that it actually explains the existence of modern organisms (well if it hasn't yet been observed, its difficult to prove its prevalent in history). Quite a difficult challenge for you.

Not if you know how to read genomes.

mindspawn writes:

You missed my point. The original clone of the E.Coli experiment already had an aerobic promoter in the rnk gene, This means that the organism was not always anaerobic, if one section of it already had a latent aerobic function.

E.coli isn't an obligate anaerobe. It can function in both aerobic and anaerobic environments. What it cannot do is grow on citrate in aerobic environments. That is considered to be one of the defining characteristics of wild E. coli. The rnk gene has another completely different function. It is not a dormant promoter of the citT gene. What happened, after some necessary potentiating mutations, was that a duplication joined fragments of rnk and another gene, citG, creating a new hybrid gene. A novel gene.

mindspawn writes:

Thus the ability of E.Coli to develop aerobic functionality is NOT NOVEL,

E. coli always has aerobic functionality. It is the ability to exploit citrate in aerobic conditions that is a novel function for it. Are you sure that you read and understood all this?

Genomic analysis of a key innovation

mindspawn writes:

it was latent, as proven by the existing aerobic promoter. Even under evolutionary assumptions, it would be obvious to an evolutionist that the aerobic ability had already evolved in the E.Coli, even if E.coli is known to be unsuitable to aerobic conditions at the moment.

Once again, it isn't "unsuitable" to aerobic conditions. It just can't grow on citrate in them, and that's one of the defining characteristics E. coli. The novel function was to be able to exploit citrate in aerobic conditions, which wild E.coli can't do. And the promoter was previously nothing to do with citrate.

mindspawn writes:

So the fact that a duplication event caused the promoter to start functioning again in aerobic conditions does not prove any novel function.

No. The duplication caused a new gene which trapped the promoter into a new function as well as continuing with its previous one.

mindspawn writes:

Really do you think nature can just make a new function from nothing??

No. It makes new function from something. Read the paper.

mindspawn writes:

Regarding your links, I do see the favorable duplications. It is therefore theoretically possible for one of the copies to mutate into a novel function. The loss of copy number shouldn't be a big problem, because a further duplication could replace it. Let's focus on novel functions then.

That means point mutations on copies. Point mutations are the most common form of mutation.

mindspawn writes:

bluegenes writes:

I think you'll find that the young earth Baramin view will require extremely high levels of mutation to account for the differences within elephants. Deceptively, Asian elephants and the mammoth are closer to each other than they are to African elephants. What'll happen if the genomes are fully sequenced, and you find that the quantity of difference between African and Asian elephants is far too great for them to have come from a bottleneck 4,500 years ago? It certainly will be.
Based on the genomes of two mammoths and some African elephants, the current estimates of the difference between the mammoths (+ Asian elephants) and the Africans is about half that of the differences between humans and chimps. Tens of millions.

Possibly. I thought the genetic overlap between mammoths and elephants was greater . But they could be two separate baramins.

They [different elephants/mammoth] could easily be separate baramins. I am not a YEC, I believe biological life was created ~6500 years ago, not the earth. There is nothing that "easily" falsifies the view, especially in this thread that we are actually dealing with. Your other points will be falsified in other threads.

There's plenty that easily falsifies the young biosphere view.

mindspawn writes:

bluegenes writes:

How do you decide what's "too different" to be related? Surely the limit should be set by the quantity of genetic differences possible in your time scale. That's so little that you'll not only have to separate the common chimps from the bonobos and us from Neanderthal, you'll have to separate Africans from Australian aborigines and have them separately created in different Edens.

Really??? Back up your comments please.

Sure. Here: Message 1

ms writes:

Neanderthals bred with humans, which indicates a very closely matching genome. And I have no problem with a bonobo and a chimp on the ark, but all humans, even Neanderthals, come from Adam.

wikipedia:
"At roughly 3.2 billion base pairs,[3] the Neanderthal genome is about the size of the modern human genome. According to preliminary sequences, 99.7% of the base pairs of the modern human and Neanderthal genomes are identical, compared to humans sharing around 98.8% of base pairs with the chimpanzee.[4] (Other studies concerning the commonality between chimps and humans have modified the commonality of 98% to a commonality of only 94%, showing that the genetic gap between humans and chimps is far larger than originally thought.)"

Difference ? 0.3 % I'm sure most of those difference are merely large inactive duplications, which can often occur.

Are you really sure?

mindspawn writes:

In just ONE generation, you can have an entire chromosome duplication, a few percent of the genome (Down's syndrome). To have a 0.3% duplication, its possible to retain fitness (unlike down's syndrome which reduces fitness).

You're suddenly very keen on big duplications which would have to contain a lot of coding genes.

Actually, if they're talking about base pairs being identical, that means they'll be talking about point mutations. That would be 10,000,000 differences. Let's work it out at a rate of 100 mutations going to fixation each generation down each line from Adam and Eve, giving us 520 generations, so 52,000 differences.
No good eh! It looks like the Neanderthal are a different baramin from us.

mindspawn writes:

Are you seriously asking why features should be grouped. I frankly think that's a childish argument being put forward often in this thread, when even under evolutionary assumptions features do converge into suitable groupings depending on functionality. So whether designed, or evolved the very functionality determines the grouped features. This is common sense, and can be seen throughout nature. Birds have lungs, bone structure, and wing structure suitable for flight. Therefore they all have these features in common with eachother.

So who would design flightless birds with wings?

ms writes:

Even out by two orders of magnitude, there should be millions of alleles in each locus. Not just 2000. So still your figures agree that the number of alleles should be numerous. But how do you define an allele? Any difference in a gene is a new allele surely? Correct me if I am wrong. You seem to be trying to differentiate between neutral mutations, but I'm not sure if they made that distinction when counting 2000 alleles in humans, they probably looked for any difference in the sequence to define a new allele.

I wasn't making a distinction, merely pointing out that on a model of neutral evolution, the variants wouldn't be found in most of the population. Nearly everyone would have the original 4 unchanged.

ms writes:

Yes. Please test that prediction. The overwhelming majority would have most of their base pairs matching the original four genes, even if demonstrating new alleles with minor mutations.

No. They would have versions of the 4 intact. Variants would only be in a minority. One seventy-thousandth of the population would receive them each generation, so in 260 generations from Adam and Eve, about 1 in 270 people would have a new variant. We could test that. It belongs on my falsification of YEC by genetics thread.

mindspawn writes:

ie Four of those genes, give or take a few point mutations in each gene. but you also have to take into account the Nephilim, beings came to earth disobediently and bred with women, their offspring would have additional genes.

Can the Nephilim been directly observed, or indirectly observed, or not actually observed in any way at all?

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