I think it’s high time we saw Shapiro’s pretty maids in action…

There are non-random mutations. Never non-random in nucleotide sequence – at least not to my knowledge, not that I know anyone else knows, and certainly not in any of the major evolutionary pathways we know – but certainly quite non-random in other respects.

Nobody is disputing this

But at heart those mechanisms for selective non-random mutagenesis evolved from random mutation and selection, random mutation and selection is still a primary driver of evolution in large part via genetic drift, the nucleotide sequences that arise in non-random mutagenic events (like horizontal gene transfer, somatic hypermutability, “hot spots,” stress induced hypermutagenesis) are still random and then selected for in some way or another (this is how the immune system works), and while they do exert non-local controls, they still arise 100% of the genome and cannot exist without it.

So nobody is questioning that these semi-non-random events occur. Shapiro’s mistake is that he thinks this deals a blow to the modern evolutionary synthesis. It does not. The modern synthesis easily takes into account these novel mutagenic pathways, they do not violate any principles of the synthesis, and they do not replace or otherwise undermine the modern synthesis.

That’s it. Nothing more than that. He is doing good science – he is correct in his observations. He is not correct about the implications of his observations.

How is the word ‘random’ used in evolutionary theory?

If we can determine what the claim of ‘random’ is in evolutionary theory, then we can look and see if any of Shapiro’s experiments bring that into question.
That is what I would like to determine.

At this point it seems they do in a number of ways- but it all depends on what is meant exactly by the term ‘random’ in the phrase ‘random mutations’. Let’s get what is meant by ‘random’ and then see if Shapiro’s claims hold any water by comparing the experiments to the claim.
OK?

Thankfully my strings are pretty short and thin, so I doubt I’ll endure much neck trauma as a result.

I say that amplification is a form of mutation and my reference is the ‘biology direct’ dictionary that defines the term –

Very well, you have used semantics to find the single exception to the “all mutations result in random nucleotide sequences.” Or did you?

The duplication event itself is random, that much is established.

How about what is duplicated? Well lets see:

Duplication results from an unequal crossing-over between misaligned homologous chromosomes during meiosis. It may involve a replication of a portion of DNA, or of an entire chromosome

Hmm… seems to me that the overall sequence of a duplication event would still be random. You can say “the sequence will be almost entirely like a portion of the genome from 1 base pair to the entirety of the genome” and that is about as specific as you can get. Precisely which part of the genome is duplicated is random. Whether it is 1% or 100% of the genome is random. Where the 1% starts and ends is random. Even the fidelity of 100% duplication is not perfect, which means the duplicated nucleotide sequence cannot be the same as the original which means… the resulting nucleotide sequence is random.

Lets do this as a simple test of the premise. Lets say I give you the entire Drosophila genome.

Now, first step – predict when a duplication event will occur. Oh right, that’s random.

Next step: let’s say a duplication event has occurred. Predict how much of the genome is duplicated. Oh, that’s random too.

OK, next step: A duplication event has occurred, it comprises 10% of the fly genome. Predict if it is heritable or not. Oh right, that’s random too.

Ok fine, next step: Duplication event has occurred, it comprises 10% of the genome, and it is heritable. That means that the fly offspring will get 110% of the DNA it normally would. Predict which 10% was duplicated. Oh, random too.

OK… duplication has occured, 10% of genome, heritable, and it is on the the R arm of chromosome 2. Predict which specific 10% was duplicated? Oh.. random again.

OK… duplication has occurred, but this time 100% of the genome, it is heritable. Predict the exact nucleotide sequence of all 279megabases. Oh, right, you can’t even do that because there is still random error in duplication due to less than 100% fidelity in transcription processes.

What I am getting at, sonic, is that all DNA copying or creation of any kind generates a random nucleotide sequence. You cannot predict the precise nucleotide sequence, or even what errors will be inserted where.

So no matter how you slice it, it is still random and the nucleotide sequence generated at the end of any mutation event, no matter how broad you decide to define that is still at heart, and usually on multiple levels random.

And what would falsify yours, I wonder?
Please stop hassling me because ‘my position’ is falsifiable and yours isn’t.

My position is falsifiable – evidence of any other mechanism for the instantiation of life that isn’t abiogenesis would falsify it.

I am hassling you because the “other” hypothesis you have been positing make no sense at a fundamental level. Either you are reiterating abiogenesis in different words or you are invoking some magical force or some non-magical force we have no reason to believe exists. In other words, you haven’t been able to formulate any cogent thought beyond “what about something other than abiogenesis?” without invoking magic or really, really far fetched ideas. And you complain that I am hassling you for such poor hypothesis generation?

Oh, and I’m going to quote the experiment that shows how life arises and you are going to say it has nothing to do with how life arises.
Enough.

Now I’ve had enough. That is such a ridiculously gross misrepresentation of my position that I am seriously just about to be done with you for now… and probably will because I leave town to have holidays with my family in less than two days anyways.

I never said that it has nothing to do with life. In fact, I clearly stated:

The evidence demonstrates that life begets life and nothing else. It does not speak on abiogenesis at all…Just because life begets life doesn’t mean only life begets life, it is just the most common way.

See there? I even said it is the most common way. But the experimental data you are so desperately clining to doesn’t explain the origin of life. It only explains how life continues and propagates and becomes more complex. That is why your only talking point is irrelevant because it doesn’t address the concept of abiogenesis or the origin of life.

How do you determine when the ad hominem applies? is the question. It seems arbitrary

Nothing arbitrary at all. It applies when it is material to the discussion. I never tried to discredit Huxley based on his theological beliefs. I was positing that his beliefs and the time period in which he lived would make his word choice in terms of “philosophical faith” different in context. Furthermore, claiming that his contemporary Christians would call him an atheist doesn’t mean anything. Ken Ham thinks Pat Robertson isn’t a True Christian (™) and that his denies the true word of god. Is Pat Robertson an atheist?

In any event it was all a tangential side point. You still haven’t addressed how the only leeway you can seem to get is by citing someone who agreed abiogenesis was likely and possible, though not proven, and died 117 years ago!. How about a legitimate scientist today?

Don’t forget – we aren’t debating the specific mechanisms of abiogenesis. We are debating the concept as a whole. I’ve already said numerous times there is no clearcut evidence which mechanism(s) actually happened, but we have enough evidence that it did and multiple lines of evidence pointing to the plausibility of gradual chemical evolution to life.

You have absolutely nothing except a lack of evidence on which to try and build a theory of your own, which you can’t even articulate properly, and involves invoking undiscovered and unpredicted “forces.” So really, who has the weaker stance on this one?

With that, I bid you (and all) adieu and very happy holidays. I will probably be much more quite on these fora until the New Year.

First off–
AHA– yes, you can claim that mutations are independent- and that is something I can completely understand and I think it is at the heart of the earlier statements I was having trouble understanding– right? (Oh, this is good!!)
If you want to apply the mathematics that is usually applied (statistics and probability aka Fisher et al) then this is an important assumption that will allow for the math to be valid.
The determination of this is difficult in reality and I believe this is part of the debate about how to interpret the results of certain experiments.
But I understand what you are saying with this and I believe this takes care of an earlier misunderstanding. Yippee!

You say an amplification is not a mutation and your reference is an article that distinguishes between ‘point mutation’ and ‘amplification’,”

I say that amplification is a form of mutation and my reference is the ‘biology direct’ dictionary that defines the term –
“Mutation
Definition (genetics)
(1) A permanent, heritable change in the nucleotide sequence in a gene or a chromosome; the process in which such a change occurs in a gene or in a chromosome.
…
Further we have this (from the biology online dictionary)-
Duplication mutation
Definition
A type of mutation in which a portion of a genetic material or a chromosome is duplicated or replicated, resulting in multiple copies of that region.
Supplement-
Duplication results from an unequal crossing-over between misaligned homologous chromosomes during meiosis. It may involve a replication of a portion of DNA, or of an entire chromosome.”

Note- in the synonyms section ‘gene amplification’ is listed specifically as a synonym for ‘duplication mutation’

I really do believe if we can get the words right the disagreements are about very specific things and there is actually a great deal of agreement. (I was in the math department– terms are defined exactly, I realize that isn’t always possible, but I’m seriously thinking f we clear up the words the disagreements and agreement will become obvious and the agreements will be big and the disagreements clarified. That’s what I’m shooting for with all the ‘word play’.
Understanding. OK?

No, I don’t have to go anywhere on abiogenesis.
I can point to the actual experimental evidence.
It is you that denies the evidence by ‘logical’ argument.

And I do know what a black swan would do to ‘my position’– falsify it.
And what would falsify yours, I wonder?
Please stop hassling me because ‘my position’ is falsifiable and yours isn’t.
It makes you look a bit foolish when you think about it.
In fact, stop calling the actual experimental evidence ‘my position’. It isn’t my position- it is the experimental evidence for crying out loud.

Oh, and I’m going to quote the experiment that shows how life arises and you are going to say it has nothing to do with how life arises.
Enough.
Imagine if the tables were turned and the results showed that life comes from chemistry.
If I then said– but that doesn’t show that the first one wasn’t from god– your experiment is inconclusive and in fact irrelevant to the question– well you would know what was behind that, wouldn’t you?
In the same way I know what is behind your claim that the experimental evidence that shows how life arises is irrelevant to the question as to how life arises.
OK?

And Huxley aka Darwin’s Bulldog, invented the term ‘agnostic’ for his religious position. And had this to say about his position as well-
“Nevertheless I know that I am, in spite of myself, exactly what the Christian would call, and, so far as I can see, is justified in calling, atheist and infidel…”
http://en.wikipedia.org/wiki/Thomas_Henry_Huxley_and_agnosticism#Thomas_Henry_Huxley

I have seen it done a few times– the dismissal of a position based on the person who is making the statements religious beliefs.
I’m trying to understand how this works–

Do you reject ‘classical physics’ on the same grounds- Newton’s beliefs?
If not, why not?
Do you reject the efficacy of vaccine based on the beliefs of Jenner and Pasteur?
If not, why not?
Do you reject ‘Planck’s constant’ due to Planck’s religious views?
How about Maxwell and electrodynamics?

How do you determine when the ad hominem applies? is the question. It seems arbitrary.
Probably like it looks arbitrary to some that i would ask for a demonstration of a claim.
You know– such an arbitrary thing to do…

http://www.biology.ewu.edu/aHerr/Genetics/Bio310/Pages/ch13pges/ch13note.html

Wikipedia abiogenesis:

http://en.wikipedia.org/wiki/Abiogenesis#Current_models

http://www.ncbi.nlm.nih.gov/books/NBK21322/

Chapter 14: Mutation, repair and recombination:

http://www.ncbi.nlm.nih.gov/books/NBK21114/

I believe a gene doubling is called an ‘amplification’ mutation.
And I think ‘amplification mutations’ include any duplication of a region of DNA that includes a gene– all the way up to and including the entire chromosome.

We conclude that amplification and mutation are independent outcomes of adaptive genetic change.
-PLoS Biology

In other words it is a short hand way of referring to the package of amplification and mutation. The amplification itself is not technically a mutation. A simple high fidelity gene or genome duplication is not considered a mutation event. If the doubling is deleterious or lethal (like say an autosomal trisomy in humans which isn’t 13, 18, or 21) then the organism dies and the process which led to the random duplication event is selected against. If it is neutral or beneficial, then one copy of the gene becomes free from selection pressure and can then have random mutations act on it for a chance at novel function.

Since independent mutation events are very unlikely to hit the exact same nucleotide site, each observed mutation should be found in only a single mutant strain. By contrast, if different strains share common ancestry subsequent to the MRCA (i.e. are not independent), by definition they will share some fraction of their mutations. Thus, detection of the exact same mutations in two or more strains constitutes a signature of non-independence.
-PloS One

I’ll make a separate post with 3 more references for you to read on about mutation and how it works.

The nucleotide sequence of a mutation is always random. Now obviously, if you are talking about a point mutation of a single nucleotide (SNP) then you have in essence a 25% chance that the random mutation will be the same in two independent mutagenic events because there are only 4 nucleotides to choose from. That is a first approximation of course, since tautomers of nucleotides can be substituted and uracil can be erroneously inserted instead of thymine, but you get the idea.

He understands his thinking abiogenesis is true is a matter of ‘philosophic faith’.
You claim there is no alternative.

I think Huxley is right on this one, my friend.
What can I say?

Do you really think Huxley would say the same with what we now know (you know, considering he died 117 years ago, before molecular science even existed)? Do you think his religious beliefs may have played a role in this? And lastly, don’t you think it funny that you have to go all the way back to Huxley to try and grasp at a straw in the abiogenesis conversation? Can’t you find someone more recent, preferably not a devout theist?

I mean really, “I think [a man who died 117 years ago] is right on [the topic of molecular interactions that didn't exist as a thought in his time]?”

Well, those are the main options that people I know consider and I’m personally willing for any of the above to be true, so

One looks to the experimental evidence to help determine the answer.
“Life comes from life,” is the result of the experiment that most closely tests the hypothesis.
This seems to indicate either 2 or 3 is likely.

No, it does not! That is NOT the way science works, sonic. The evidence demonstrates that life begets life and nothing else. It does not speak on abiogenesis at all. Seriously, it doesn’t. This is why we are having such a hard time with the conversation.

You are making the argument that because all the swans you have ever seen are white, that all swans must be white and only white. You are not even considering what a single black swan would actually do to your argument.

Just because life begets life doesn’t mean only life begets life, it is just the most common way. One single instance of abiogenesis in all of the universe in 13 billion years completely shatters your thesis. Never mind the evidence and a priori plausibilities we have in place to demonstrate validity to the thought of abiogenesis.

But this doesn’t disprove 1. No, many people who have studied the issue have decided that life does come from inanimate matter. They have good reasons for this determination too.
Yet, when asked to demonstrate the claim, they only promise that it will be forth coming.
The claim remains unsubstantiated.

Just look at the wikipedia article on the topic. It lists all the experiments and thoughts on it. I’ve said it before, and I’ll say it again: we do not have conclusive empirical proof of a specific pathway leading to “life” but we do have numerous experiments demonstrating that all the complex organic components of life can and do form spontaneously from simpler inorganic molecules in an open thermodynamic system. We have proof that these can also spontaneously assemble and replicate. We have no evidence that any physical laws or fundamental forces we have discovered would preclude this. We have evidence that there was ample time for this to happen gradually. And of course, we have evidence that there is life here and at one time there wasn’t. While this doesn’t “prove” abiogenesis happened, it demonstrated so many pathways and so much plausibility that it would be perverse to think something else happened. Sometimes perverse ideas pan out (like microbes living in the lining of your stomach causing ulcers) but most of the time they don’t. And until you (or someone) comes up with a perverse idea that explains things better than abiogenesis and doesn’t include magic (godidit) any reasonable person should provisionally accept abiogenesis as the best hypothesis with the vast preponderance of evidence supporting it. In other words, no need to wait for more evidence – we have plenty enough to accept the hypothesis as reasonable scientists and pursue specific mechanisms in our research. In other words, we aren’t doing research to prove abiogenesis, we are doing research to determine the possible and most likely ways in which it did happen on the reasonable assumption that it has.