Moran on Sternberg: What Biologists Mean by "Math Errors"

Continuing the discussion from Theman8469’s Complaints about Nathan Lents:

The original quote from Sternberg…

The segments of our DNA that are commonly called “genes” consist of protein-coding exons and non-protein-coding introns. Initially, the entire DNA segment is transcribed into RNA, but between ninety and ninety-five percent of the initial RNAs are “alternatively spliced.”

What is alternative splicing? Imagine that the initial RNA derived from its DNA template has the organization A—B—C—D—E—F, where the letters represent blocks that specify amino acid sequences and the dashes in between the letters stand for introns. Alternative splicing enables multiple proteins to be constructed given the same RNA precursor, say, ABCDF, ACDEF, BCDEF, and so forth. In this way, hundreds or thousands of proteins can be derived from a single gene.

There’s more. The messenger RNAs that are produced by this process—and therefore the proteins that are made in a cell—are generated in a way that depends on the stage of development as well as the cell and tissue type. In the above example, a nerve cell may express the ACDEF version of a messenger RNA whereas a pancreatic cell may produce only the BCDE version. The differences are biologically essential.

What does this have to with introns? Everything. It is the presence of introns that makes this permutative expansion of messenger RNAs possible in the first place.

So let’s do the math. At least ninety percent of gene transcripts undergo alternative splicing, and there are at least 190,000 introns in the human genome. That means we have at least 0.90 x 190,000 = 171,000 introns that participate in the alternative-splicing pathway(s) available to a cell.

http://www.evolutionnews.org/2010/06/mathesons_intron_fairy_tale.html

Larry Moran responds:

Sandwalk: Creationists, Introns, and Fairly Tales

It’s up to you, dear readers, to figure out all the things wrong with this explanation. You can start with the math. Arithmetic isn’t one of their strong points. Or maybe it’s an understanding of biology that’s the real weak point?

@theman8469 rightly protests that 0.90 x 190,000 really does equal 171,000. Larry knows this too. That is not what biologists mean by “math errors”, though I fully admit this is our idiosyncratic way of talking. We often say that some one is making a “math error” when they are computing the wrong quantity with the wrong assumptions at play. This is not really an “arithmetic” error, even though we often say it is. Rather, it is an error in mathematical modeling.

This is how Larry explains it when pressed on this…

There are two important problems with Richard Sternberg’s article.

First, it’s almost certainly not true that 90-95% of all human protein encoding genes exhibit alternative splicing. While there’s no consensus right now, the majority of biochemists think this number is too high. Whether it’s 5% (my guess) or 50% (a common estimate) is controversial.

Sternberg gives us no indication that he understands this controversy. He bases his entire fairy tale on a value that has been pretty much discredited.

His second problem is not even understanding the consequences of his false assumption. Let’s assume that Sternberg is correct and 90-95% of all protein encoding genes exhibit alternative splicing. Since there are 20,500 such genes in our genome it follows that about 19,000 are alternatively spliced.

The minimum requirement for alternative splicing is that an intron can be included or excluded in the mRNA. The lower limit for the number of introns is thus 19,000 (actually 18,450 - 19,475).

In other words, as many as 171,000 introns could be (mostly) useless junk. It will be even more if we accept a lower number of alternatively spliced genes.

I don’t think this is the message that Sternberg meant to convey in his posting. This is why we call them IDiots.

BTW, Sternberg took the 190,000 introns information from Stephen Matheson who quotes a 2005 paper by Fedorva and Fedorov. According to those authors, there are 23,506 protein encoding genes in our genome of which 21,746 contain introns. Thus, the average number of introns per gene is greater than 8.

We now know there are fewer genes and the total number of introns has been dropping steadily as workers begin to eliminate spurious introns when genes are annotated. I think there are about 150,000 introns (see: Junk in Your Genome: Protein-Encoding Genes).

The exact number doesn’t matter so much but the point is you can’t mix and match numbers. It’s invalid to use a lower estimate of introns per gene (e.g. 7.6) with a high estimate of the number of introns (e.g. 190,000).

Notice, at no point does Moran question that 190 x 0.9 = 171. Rather, he is questioning the premise of the calculation, saying the wrong numbers are being multiplied together and that Sternberg is making a poor estimate.

I entirely grant that this is not, literally, an “arithmetic” error in the most strict of senses. Though, plugging the wrong numbers into a formula is sometimes called on an “arithmetic” error. Errors in mathematical reasoning or modeling, like this, are often called “math errors” by biologist. That is our jargon. Yes, it can lead to confusion. I wonder though if similar jargon is found among @physicists.

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Way back when, @art was part of this conversation too.

We are going around in circles here. If you can reference one scientist (even a biologist), other than Moran, who uses the term “arithmetical error” when dealing with, the perceived, failings of a mathematical model with incorrect data - please let me know.

You are right about physicists using terms incorrectly. My personal bugbears are “infinity” and “nothing”. The first is pretty harmless but the second is not and has metaphysical implications. Some, and I mean only some, physicists confuse “nothing” as in non-being, with “nothing” as a particleless quantum space (think of an empty box with interacting fields) I know exactly what they mean. When Kruass was caught out of this by Craig, Albert and Mauldin he claimed he was using the physicists definition but this completely undermined the whole thesis of his work (where did the quantum space come from, the fields, mathematical structure). He was letting the two interpretations of the term “nothing” lapse into one other leading to a metaphysical contradiction.
Moran frequently dismisses all religious people as idiots and deluded. In this post he clearly differentiates between math (which if you stretch it could well include modelling and data input and I have no problem with it) and arithmetic; he clearly implied that Sternberg was incapable of basic number manipulation. Perhaps this was just a case of bad writing on Moran’s part but I doubt it - the anti-ID crowd are a non-thinking crowd.
My challenge stands, reference a scientist who uses “arithmetic” to mean bad modelling and data input. I will have learned something.

Moran did not say “arithmetical error”. He said “mathematical error”. Those are not the same.

Yes, you interpreted it as an arithmetical error. But “mathematical error” is a broader term.

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Moran did not say “mathematical error”. Are all biologists insufferably stupid? Or are they so committed to the ‘brotherhood of biologists’ that they lie, squirm and distort to protect one of ‘brotherhood’? Come back when you gain the ability to read and quote correctly.

By the way I replied to the Mayer/peptidyl transferase issue.

As promised I have read Stephen Meyer’s Signature of the Cell. I doubt that Mercer has read it, as there are many other ‘gotcha’ moments – spelling mistakes as well that he could have focused on as well. For example in I chapter 3 Meyer incorrectly writes ‘virus’ (page 66) instead of ‘bacteria’ but goes on to correctly apply the term ‘bacteria’ correctly multiple times later in the chapter. Clearly this is just a typo or proof reading error.

Meyer in one place also uses a variant spelling of ‘spliceosome’ as ‘splicesome’ but uses the orthodox spelling elsewhere. Once again Typo or proof reading error but does not impact on the rest of the book at all.

The peptidyl transferase issue comes up in this passage

“a protein within the ribosome known as a peptidyl transferase then catalyzes a polymerization (linking) reaction involving the two (tRNA-borne) amino acids. In the process, the first amino acid detaches from its tRNA and attaches to the second amino acid, forming a short dipeptide chain. The ribosome then ejects the first and empty molecule and moves along to “read” the next triplet of bases on the mRNA. Another tRNA–amino acid carrier pairs with the next mRNA codon, bringing a new amino acid into close proximity with the growing chain, and the process repeats itself until the signal for termination is reached on the mRNA. Then a protein termination factor, rather than an aminoacyl tRNA, binds to the second ribosome site and catalyzes hydrolysis (dissolution) of the bond holding the peptide chain to the tRNA at the first ribosome site. The newly assembled protein then detaches.”

There is nothing wrong with this passage apart for the incorrect identifying the peptidyl transferase as a protein. The rest of the book, when dealing with the the peptidyl transferase focuses on its function, so Meyer has no opportunity to reidentify. However both the text and the references he cites does clearly indicate a correct working knowledge of the peptidyl transferase. I would say that this is a proof-reading error as the book is full of them and Meyer’s demonstrated correct understanding of its functioning.

Meyer has not been challenged on this so unlike Lents has not defended a false statement as true when it is corrected. The funny thing is that no one has brought up the peptidyl transferase when engaging with Meyer: not Darrell Falk, not Arthur Hunt or even Steve Matheson. I am sure that even these odd individuals recognize a typo when they see it.

He said “You can start with the math.”

Yes, he also used the word “arithmetic”. But you are still interpreting him too narrowly. The discussion in the comments of that “Sandwalk” post make it clear what were his concerns.

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OK let us unpack this in such away that gives both you and Swamadass a way out and then see how Swamadass falls straight back in.

Original quote

“You can start with the math. Arithmetic isn’t one of their strong points. Or maybe it’s an understanding of biology that’s the real weak point?”

Both you and Swamadass want to extend the term ‘math’ to include both mathematical modelling and data input. I think it is a bit strange, especially the second bit. But as I said I am fine with it; a certain functional lack of rigour is perfectly acceptable for the working scientist. Also most scientific disciplines have their own esoteric interpretations of terms – again fine. Moran then claims that “arithmetic” is not one of their strong points. I do not think that Moran is using ““arithmetic” as a synonym or a substitute for “math” (if he is why use it?). If he is, then he has also widened the term so broadly that it almost loses its meaning as a descriptive term. Of course, in addition, it does not allow ““arithmetic” to refer to a proper subset of mathematics. Note I am not restricting the term to, say number theory, but merely pointing out that some “math” is not “arithmetic” but

all ““arithmetic” is “math”.

This is first part of the disjunction. The second part is “or…understanding of biology that’s the real weak point?”. Now all disjunctions are and/or and it appears that Moran’s concerns are with a faulty understanding of the data and the modelling around it and not with the actual computations themselves (the number crushing) which are correct. Note, that Moran is using this disjunction to make a distinction between arithmetic and biology. One does not cross over to the other. Note also that if the biology was correct, then there would be no problem with the “math” and as arithmetic is a subset of math, with the arithmetic.

Swarmadass suggests that “Arithmetic error” is used (“our Jargon”) to cover plugging wrong numbers into a formula. I doubt it but you never know and I am sure Swamidass will be able to enlighten me with some evidence. But I have read several books and papers on mathematical biology and have never seen “arithmetic” used this way.

However this is not how Moran sees it, as Moran’s disjunction shows. Moran’s comments all deal with the second part of the disjunction as I said.

Personally I think that Moran was just pushing the fact that he thinks ID’ers are Idiots. He also has a track record of calling religious people stupid and deranged -he was just continuing here in the same style.

This started as people were commenting about how off-hand comments or typos render people, who you disagree with, as lacking in knowledge. I was pointing out that anyone can play the same game. When I read Moran’s post I did not think that he was numerally illiterate – just rude.

18 posts were split to a new topic: Pointless Arguing Before Theman Was Silenced

Pick one.

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No, we just have a different jargon than you are used to, and I freely admit it can be hard to follow. I also agree that there is no reason for you to adopt our jargon. I understand why Moran was unintelligible to you, but he also exaplained precisely what he meant in the comment.

What more do you want? What exactly is your point? What still remains a point of disagreement? I can’t really tell.

As for the term IDiot, I never use it (except when referring to the term). I do not think it helps his case and I wish he would stop.

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Learn to read in context my dear evograd. It reminds me of the old classic “Have you stopped beating your wife?”. I was responding to the fact that making a mistake, typo, ill-informed statement etc. does not render that individual incompetent. I was mirroring comments that follow the ‘gotcha’ type of argument that follow the logical form

If x makes a (typo, mistake etc), then x lacks knowledge.
x makes a ((typo, mistake etc)
Therefore x lacks knowledge.

Of course in the place of “lacks knowledge” we have something stronger. I mirrored that type of argument to expose it.

I know that biologists are usually tested as having IQ’s 8 to 10 points lower than physicists, mathematicians and philosophers. I think that data (arithmetic?) must be wrong as the biologists, if a fair representative of those posting on this site is any indication, it appears to be a lot lower.

So when you said “Moran is numerically illiterate”, you were just “playing along”? A simple yes or no would suffice.

Were you trying to describe “affirming the consequent” and got things backwards? Affirming the consequent follows the form:

If X, then Y.
Y.
Therefore X.

So the argument I think you’re trying to describe would be “incompetent people make mistakes/typos. Person A made a mistake/typo, therefore they’re incompetent”.

I agree that this can be a fallacious argument, it depends on the types of mistakes/typos. If someone claimed to be a geneticist and yet consistently misspelled “cytosine” as “cytozeen”, that would be a pretty big red flag, don’t you think?

To quote @NLENTS:

Or if someone writes a chapter titled “The RNA World” and concealed the strongest evidence supporting that hypothesis from his readers by claiming that the most important ribozyme in biology is a protein?

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You previously objected to Larry Moran using the expression “IDiot”. I agree that Larry should stop using that expression. But doesn’t the same thing apply to your comments about the IQ of biologists?

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