DNAunion

DNAunion: Principia, you might want to review this board's rules.

DNAunion

DNAunion: And the take-home point is...

DNAunion

DNAunion: Sure, what's 11 orders of magnitude between friends!

Principia

RA,
You have to understand Rode's point first. The underlying point that he is trying to make (ignoring for the moment how he makes it) is that SIPF dipeptide yields show similar distributions to dipeptide distributions found in archaebacteria. Now, what he used as a statistic was simply to count the number of similarities between SIPF and archaebacteria dipeptides amongst the top four yields. As I pointed out, this is a poor statistic to use. And if it is a poor statistic, it really doesn't matter how one goes about fixing the probability analysis based on that statistic (especially when the fix is incomplete).

PS: that above is the take-home point, folks -- and for clarification read my first post on this thread.

PS2: probability analysis or not, one only needs to look at the data to get an intuitive sense of whether or not Rode is justified in his conclusions. One can say, I suppose, that a decent statistical analysis is merely icing on the cake here. I am still waiting to hear why 1e-7 is such a bad value so as to invalidate Rode's conclusions.

DNAunion

DNAunion: I've got a great idea. Principia, you have access to the Rode paper. Why not show us what the real probability is and exactly how you get it.

pz

Don't start this.

I don't see any instances of inflammatory speech that require moderation here. If you do have a problem with what someone else has said, use the "report this post to moderator" link, preferably with a specific explanation of your objection.

RufusAtticus

I got that much. I guess, I'm just still trying to figure out exactly what probability he was looking to compute. It does seem rather sloppy. I'm going to do some calculations from his data and get back to this thread.

Edit to add:

Can anybody figure out what Rode means by "Ala=leu" in Table 8?

Principia

RA,

I am guessing for the moment that it means approximately equal distributions. What I'd really like to know are the numbers besides the SIPF ones that Rode used (e.g. the archae dipeptide distributions).

Let me see if I can track them down.

DNAunion

DNAunion: I’m still trying to get a handle on Principia’s point here.

Principia has said now, half-heartedly, that the programming language used wasn’t material. So we can discard his “funny” comment about Visual FoxPro.

DNAunion: Well, Principia hasn’t yet pointed out any flaw in my code (nor do I imagine he will in the future).

If it’s not the language that was used, and it also wasn’t about bugs in my program, it appears that Principia’s point is simply that he personally feels it is “unscientific” for me to write a program to do something that can be done by hand. If so, he overlooked several things.

For example, what about the more involved calculations I brought up? I could do the simple ones by hand but was at a loss as to how to do the more complex ones. So I guess Principia considers a person’s creating a tool to work out problems that he/she can’t do otherwise to be “unscientific” (sounds like being resourceful to me).

And speaking about those more involved calculations, I asked Principia to show me how to do one. Instead of replying to my sincere request for help in a positive manner, Principia has seen fit to spend his time being acrimonious toward me (one has only to contrast Principia’s response to my question about algebra to that of the other two respondents to see that this is so – of course, other examples in this thread also support this position). Gee, I wonder if Principia considers being condescending and caustic as being “scientific”? (maybe it is, as long as you don’t write computer code while being like that!)

In light of Principia’s unwillingness to show me/us the more scientific way of skinning this cat, despite my request, I guess I will just have to make some assumptions about his point.

For example, I’ll assume that Principia is unaware that the program I wrote can handle just about any combination of parameters one might throw at it. Want to return tiles to the urn after they are selected (replacement)? Simply change the variable nDiscardTilesOnceChosen from 1 to 0. Want to have 20 tiles, or 15 tiles, or 6, instead of 9? Simply change the variable nLetteredTiles. Want to have 12 targets, or 2 targets, or 7, instead of 4? Simply change the variable nTargetTiles. Want to have more trials per iteration, or more iterations? Just change the appropriate variable. Therefore, this program extremely flexible and has far broader uses than this one SIPF calculation. I guess Principia considers broad applicability to be “unscientific”.

In addition, once the code is setup and debugged, the results are guaranteed to be correct – first time, last time, every time - no matter what combination of parameters one uses. But each time someone does such a calculation by hand, there is a chance that an error will sneak in somewhere and the result will be off. I guess Principia considers guaranteeing ‘accurate’ results to be “unscientific”.

Furthermore, I can reuse this program time and time again. Principia will have to perform the calculation by hand each time he wants to be “scientific”. So I guess Principia considers reusability to be “unscientific”.

Also, I can hand a copy of the program to someone else and they then can immediately calculate a wide range of probabilities – even if they are at a complete loss on how to do so by hand. I guess Principia considers the ability to empower others – providing them with a useful tool that allows them to perform calculations they otherwise could not - to be “unscientific”.

So I think I see Principia’s point to #4 now. It was foolish of me to have created a tool that expanded my capabilities, has broad applicability, is reusable, is guaranteed to produce ‘accurate’ results, and has the ability to empower others. I don’t know what I was thinking.



Lab's closing - that's all for today.

Principia

All I have to say to debunk the entire post above is that DNAunion is not me, and therefore does not speak for me, nor knows what I think. I could also simply point him to my first post on this thread which addresses most of his concerns adequately. But I see nowhere in his post any indications that he reads to understand.

But one thing is for sure -- DNAunion is quite upset today. I'll let him cool off.