Is science just another religion? (and so much more..)

#61
I do not think the discussion about whether or not frame shift is in play negates the value of Nylonase as evidence for recent new function.
This essay:
Is it easy to get a new protein? A reply to Ann Gauger
goes more in to that.

But again you answer a post with several links to good peer reviewed research, with a post on a ID/creationist blog, run by the Discovery Institute.
My main argument in my previous post did not hinge on Nylonase in any way.
The whole issue here is about which side is staying closer to the science. If you want to decide that the orthodox side is automatically to be preferred, then you need go no further. If you want to understand this at the level of who has most authority, then fine - you have your answer. However, remember that Douglas Ax did research at Cambridge University in the LMB, so he isn't exactly a nobody in his field.

He wants to actually test whether evolution by NS can actually achieve the evolution of proteins - rather than take the concept of evolution by NS as axiomatic. It sure isn't obvious that this is remotely possible, but surely a true scientist would applaud this effort to answer the question decisively.

The core of this is that if a stretch of DNA resulted from a frame shift, it will be basically random at that point - the bases are read 3 at a time, and if you remove one base, the result is read in an utterly different way - in effect you will have jumped to a random point in protein space

Reading your last link, I'd say the situation is pretty confused, and not all the commentators are supportive of his argument. However, this nylonase question was originally raised as a slam dunk reason to believe that functional proteins can be easily be found in 'protein space'. I'd have thought that this must at least be an open question at this time. At one point he says
For even if functional sequences are rare, they may be clustered together – in which case, getting from one functional protein to the next won’t be so hard, after all.
Well 'may be' isn't very definite!

It seems to me that more research to determine just how easy it really is to mutate a protein into another one with a different function would be useful. The nylonase example seems too bound up in the history of this particular bug before anyone had a reason to take an interest in it!

The E. coli long-term evolution experiment looks intreesting, but I can't read it immediately - my brain is filling up!

BTW, I often edit a post just after putting it up - it is much easier to read on the forum with all the quotes processed etc - so I usually review my posts and ass extra stuff.

Edit: Thinking about it, the idea that useful proteins are common in protein space, makes you wonder why these need the whole mechanism of a code that codes for 20 different amino acids in exact sequence. I mean I know that from the strict materialist viewpoint one shouldn't talk of needs - but if proteins are easy to find wouldn't you think a rather less extravagant mechanism would have evolved?

David
 
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Bart V

straw materialist
Member
#63
Edit: Thinking about it, the idea that useful proteins are common in protein space, makes you wonder why these need the whole mechanism of a code that codes for 20 different amino acids in exact sequence. I mean I know that from the strict materialist viewpoint one shouldn't talk of needs - but if proteins are easy to find wouldn't you think a rather less extravagant mechanism would have evolved?

David
This seems to illustrate, so strikingly, the difference between goal oriented design and blind evolution.

Of course the path that evolution took to get to this point does not look the most logical one. It doesn't because this point was never a goal!
we just got us here step by step, and the "here" we are talking about is certainly not an end point.
There is no direction from one step to the next. Sometimes the use of informal language, to describe what evolution does, tends to anthropomorphize the process.
Although maybe unavoidable, this is something we have to be aware of.

It surprise me to see you make such an observation, because the kludginess of evolution is often used as an argument against design, maybe there is still hope.

A well know example is the laryngeal nerve:



I will try to answer more of your post later, David, but i did not notice this edit before, and i really struck me.
 

Bart V

straw materialist
Member
#65
The whole issue here is about which side is staying closer to the science.
Ok, let us take a look at that.
The “Hard-to-Get-a-Protein” hypothesis (HGP for short) seems to be largely based on the 2004 Axe paper
Estimating the prevalence of protein sequences adopting functional enzyme folds.
A paper that in itself, according even to the critics of it's use, is good scientific work, but it has a very limited scope.
The experiment it describes, is very specifically about a weaker, temperature sensitive, version of one enzyme.

The claim of HGP diverges from the science when this paper is used by the Discovery Institute to extrapolate the results of this experiment to any protein, and thus estimate the chance the chance of getting any new protein at the very low number of one in 10(77).

In the various outlets run by the DI, this number is often repeated, always with the conclusion attached to it that there was simply not enough time for evolution to happen.
A conclusion that is wrong in it's reliance on the Axe paper, and is wrong on the level of it being a negative argument.
The stating of a negative argument with such great certainty, in a matter that deals with a great deal of uncertainties makes this argument very weak.


If you want to decide that the orthodox side is automatically to be preferred, then you need go no further.
This has nothing to do with orthodoxy, this is about the correct use of science, and logic.
If you want to understand this at the level of who has most authority, then fine - you have your answer.
This is also not about authority, again, this is about what is in the scientific literature.
The DI relies on one paper that does not even say what they think it says, while in the scientific literature there are many papers to find that point to the possibility of much easier pathways through protein space.
I gave you a bunch of examples in post #58
However, remember that Douglas Ax did research at Cambridge University in the LMB, so he isn't exactly a nobody in his field.
Again the scientific validity of his 2004 paper is not in question, nor is his academic standing.
For someone who does not want this to be about authority, it is strange to see you make a first class argument from authority.

He wants to actually test whether evolution by NS can actually achieve the evolution of proteins - rather than take the concept of evolution by NS as axiomatic.
Evolution by NS is not taken as an axiom, it is simply a conclusion that is evident from the data.
As with everything in science, this conclusion is provisional , but i believe the evidence needed to change this would need to come from something completely new, an unknown unknown.
As said above what Axe tested with his experiment, has a very limited scope.
It sure isn't obvious that this is remotely possible, but surely a true scientist would applaud this effort to answer the question decisively.
I disagree, the positive evidence for easier to get proteins, given throughout this thread, bring the evolution of new proteins firmly within the realm of possibility.
And the true scientists are trying very hard to answer the questions about what the various mechanisms are that make this evolution possible.

But if you want to talk axiom, or dogma, i can not believe you give the DI a free pass, they have dogma written in their DNA, so to speak.
They do not "only question" evolution.
Evidence for that is the factitious nature of the two pronged tactic they apply here. Axe publishes a good, but ultimately agnostic on the matter of ID/creationism, paper in a reputable peer reviewed journal.
So the DI can use it as evidence in blogposts, or "papers" in their in house journal.
And even in quoting Axe, they do not seem to be very honest , from this:
Meyer relies heavily on a new paper by Axe published in the Journal of Molecular Biology. Meyer alleges that Axe (2004) proves that, “the probability of finding a functional protein among the possible amino acid sequences corresponding to a 150-residue protein is similarly 1 in 10^77.” But Axe’s actual conclusion is that the number is “in the range of one in 10^77 to one in 10^53” (Axe 2004, p. 16). Meyer only reports the lowest extreme. One in 10^53 is still a small number, but Meyer apparently didn’t feel comfortable mentioning those 24 orders of magnitude to his reader.
I will leave the question of Axe's intentions open, but i am sure, the DI are not out to question anything.
They are out to advocate ID/creationism, no matter what the science says.

So, David, given all that, i would really like to know, has this conversation changed your stance on the "hard to get protein" argument in any way?
Do you think the DI would ever remove this argument from it's repertoire?
 
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