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Thomas A. Christensen II 2019-09-28 11:00:44 -07:00
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@ -6,28 +6,47 @@ motto: Keep EPDs Real
--- ---
<p> <p>
In the <a href="https://podcasts.apple.com/us/podcast/selection-for-milk-in-the-cowherd-how-much-is-too-much/id964198047?i=1000431062519">March 4, 2019 episode of BeefWatch Podcast</a>, Dr. Travis Mulliniks of the University of Nebraska-Lincoln presented the research he conducted and published in <a href="https://doi.org/10.2527/tas2016.0006">"High milk production decreases cow-calf productivity within a highly available feed resource environment."</a> In the
In the paper, he discovered that milk production in beef cattle has no correlation with calf weaning weights, but has a significant negative correlation with breedback rates. <a href="https://podcasts.apple.com/us/podcast/selection-for-milk-in-the-cowherd-how-much-is-too-much/id964198047?i=1000431062519">March 4, 2019 episode of BeefWatch Podcast</a>,
Dr. Mulliniks' paper is in agreement with several others on this topic, and was by far the largest and most conclusive study to find these results. Dr. Travis Mulliniks of the University of Nebraska-Lincoln presented the research he conducted and published in
<a href="https://academic.oup.com/tas">Translational Animal Science</a> titled
<a href="https://doi.org/10.2527/tas2016.0006">"High milk production decreases cow-calf productivity within a highly available feed resource environment."</a>
In the study, he discovered that fluid milk production in beef cattle has no correlation with calf weaning weights, but has a significant negative correlation with breedback rates.
Dr. Mulliniks' paper is in agreement with several others on this topic, and appears to be the largest and most conclusive study of this topic to-date.
</p> </p>
<p>At the conclusion of the podcast episode, Dr. Mulliniks stated</p> <p>At the conclusion of the podcast episode, Dr. Mulliniks stated</p>
<blockquote>As producers looking at bulls: we highly suggest, in our environment in Nebraska, from an Angus standpoint, an EPD of 22 or lower. ... Above that we start seeing an increase in that milking potential. But it's something that we really need to pay attention to, 'cause as our costs continue to go up, and we're not necessarily seeing an increase in the output. ... We really need to manage and moderate milk in a lot of our cow-calf setups.</blockquote> <blockquote>As producers looking at bulls: we highly suggest, in our environment in Nebraska, from an Angus standpoint, an EPD of 22 or lower.
&hellip;
Above that we start seeing an increase in that milking potential. But it's something that we really need to pay attention to,
'cause as [<em>sic</em>] our costs continue to go up, and we're not necessarily seeing an increase in the output.
&hellip;
We really need to manage and moderate milk in a lot of our cow-calf setups.</blockquote>
<p>Mathematically, he is saying:</p> <p>Mathematically, he is saying:</p>
<a href="https://www.codecogs.com/eqnedit.php?latex=\inline&space;\small&space;High\&space;Fertility=Low\&space;Milk\&space;Production=Low\&space;MILK\&space;EPD\neq&space;Low\&space;Weaning\&space;Weights" target="_blank"><img class="img img-responsive math" src="https://latex.codecogs.com/svg.latex?\inline&space;\small&space;High\&space;Fertility=Low\&space;Milk\&space;Production=Low\&space;MILK\&space;EPD\neq&space;Low\&space;Weaning\&space;Weights" title="\small High\ Fertility=Low\ Milk\ Production=Low\ MILK\ EPD\neq Low\ Weaning\ Weights" /></a> <img class="img img-responsive math"
src="https://latex.codecogs.com/svg.latex?\inline&space;\small&space;High\&space;Fertility=Low\&space;Milk\&space;Production=Low\&space;MILK\&space;EPD\neq&space;Low\&space;Weaning\&space;Weights"
title="\small High\ Fertility=Low\ Milk\ Production=Low\ MILK\ EPD\neq Low\ Weaning\ Weights" />
<p><em><strong>WHAT!?!</strong></em></p> <p><em><strong>WHAT!?!</strong></em></p>
<p> <p>
The MILK EPD is calculated from calf weaning weights. The <a href="https://www.angus.org/Nce/Definitions.aspx">Angus Association sort of admits it</a>, the <a href="http://nbcec.org/producers/sire_selection/manual.pdf">National Beef Cattle Evaluation Consortium knows it</a>, and professors in both <a href="https://www.worldcat.org/search?q=isbn%3A9781845939816">Scotland</a> and <a href="https://www.worldcat.org/search?q=isbn%3A0646387138">Australia</a> teach students how to calculate it. His research did state that
</p>
<img class="img img-responsive math"
src="https://latex.codecogs.com/svg.latex?\inline&space;\small&space;High\&space;Fertility=Low\&space;Milk\&space;Production\neq&space;Low\&space;Weaning\&space;Weights"
title="\small High\ Fertility=Low\ Milk\ Production\neq Low\ Weaning\ Weights" />
<p>
But the MILK EPD is calculated from calf weaning weights, and weaning weights only. The
<a href="https://www.angus.org/Nce/Definitions.aspx">Angus Association sort of admits it</a>,
the <a href="http://nbcec.org/producers/sire_selection/manual.pdf">National Beef Cattle Evaluation Consortium knows it</a>,
and professors in both <a href="https://www.worldcat.org/search?q=isbn%3A9781845939816">Scotland</a>
and <a href="https://www.worldcat.org/search?q=isbn%3A0646387138">Australia</a> teach students how to calculate it.
It is a maternal trait, and is not a &quot;direct&quot; predictor of weaning weights, but
<b><em>the only phenotype data that is incorporated into the calculation is that of weaning weight</em></b>.
Mathematically, that means: Mathematically, that means:
</p> </p>
<a href="https://www.codecogs.com/eqnedit.php?latex=\inline&space;\small&space;Low\&space;MILK\&space;EPD=&space;Low\&space;Weaning\&space;Weights" target="_blank"><img class="img img-responsive math" src="https://latex.codecogs.com/svg.latex?\inline&space;\small&space;Low\&space;MILK\&space;EPD=&space;Low\&space;Weaning\&space;Weights" title="\small Low\ MILK\ EPD= Low\ Weaning\ Weights" /></a> <img class="img img-responsive math" src="https://latex.codecogs.com/svg.latex?\inline&space;\small&space;Low\&space;MILK\&space;EPD=&space;Low\&space;Weaning\&space;Weights" title="\small Low\ MILK\ EPD= Low\ Weaning\ Weights" />
<p>
Of course, Mulliniks' research said very clearly:
</p>
<a href="https://www.codecogs.com/eqnedit.php?latex=\inline&space;\small&space;Low\&space;Milk\&space;Production\neq&space;Low\&space;Weaning\&space;Weights" target="_blank"><img class="img img-responsive math" src="https://latex.codecogs.com/svg.latex?\inline&space;\small&space;Low\&space;Milk\&space;Production\neq&space;Low\&space;Weaning\&space;Weights" title="\small Low\ Milk\ Production\neq Low\ Weaning\ Weights" /></a>
<p> <p>
So both of these pieces of information lead to something more like: So both of these pieces of information lead to something more like:
</p> </p>
<a href="https://www.codecogs.com/eqnedit.php?latex=\inline&space;\small&space;High\&space;Fertility=Low\&space;Milk\&space;Production\neq&space;Low\&space;MILK\&space;EPD=Low\&space;Weaning\&space;Weights" target="_blank"><img class="img img-responsive math" src="https://latex.codecogs.com/svg.latex?\inline&space;\small&space;High\&space;Fertility=Low\&space;Milk\&space;Production\neq&space;Low\&space;MILK\&space;EPD=Low\&space;Weaning\&space;Weights" title="\small High\ Fertility=Low\ Milk\ Production\neq Low\ MILK\ EPD=Low\ Weaning\ Weights" /></a> <img class="img img-responsive math" src="https://latex.codecogs.com/svg.latex?\inline&space;\small&space;High\&space;Fertility=Low\&space;Milk\&space;Production\neq&space;Low\&space;MILK\&space;EPD=Low\&space;Weaning\&space;Weights" title="\small High\ Fertility=Low\ Milk\ Production\neq Low\ MILK\ EPD=Low\ Weaning\ Weights" />
<p>I contacted Mulliniks and asked him if there was something I missed. He replied</p> <p>I contacted Mulliniks and asked him if there was something I missed. He replied</p>
<blockquote> <blockquote>
The milk EPD is actually associated with milk production. The milk EPD is actually associated with milk production.
@ -58,7 +77,6 @@ motto: Keep EPDs Real
</p> </p>
<p> <p>
He knew the answer to that, too. It turns out that EPDs are generated by computers that take into account <b>all</b> of an animal's relatives, from his sons and daughters to his distant cousins. He knew the answer to that, too. It turns out that EPDs are generated by computers that take into account <b>all</b> of an animal's relatives, from his sons and daughters to his distant cousins.
It reminded me of the Yahtzee game that was installed on my computer.
That answer didn't satisfy me. That answer didn't satisfy me.
If you're reading this, I'm guessing that answer doesn't satisfy you, either. If you're reading this, I'm guessing that answer doesn't satisfy you, either.
</p> </p>
@ -112,18 +130,18 @@ motto: Keep EPDs Real
From that day forward, I read everything I could get my hands on about EPDs, and asked anyone who might know something about how they were calculated. From that day forward, I read everything I could get my hands on about EPDs, and asked anyone who might know something about how they were calculated.
Every time it was the same non-answers that the semen rep had used: usually his exact language. Every time it was the same non-answers that the semen rep had used: usually his exact language.
What they all amounted to was &quot;you don't need to know <b>how</b> EPDs are calculated, you just need to know that they work.&quot; What they all amounted to was &quot;you don't need to know <b>how</b> EPDs are calculated, you just need to know that they work.&quot;
It was almost like I was asking sacrilegious questions, like Martin Luther of his bishops. It sounded like I had stumbled into a cult.
Every time I was rebuffed, I grew even more upset at those who perpetuated these hand-waving definitions.. Every time I was rebuffed, I grew even more upset at those who perpetuated these hand-waving definitions..
</p> </p>
<p> <p>
I eventually learned how EPDs were calculated after all. In a chance encounter at a library in a far-away state, I read <a href="https://www.worldcat.org/search?q=isbn%3A0646387138"><em>Animal Breeding: Use of New Technologies</em> by Brian Kinghorn, Julius van der Werf and Margaret Ryan</a>. I eventually learned how EPDs were calculated after all. In a chance encounter at a library in a far-away state, I read <a href="https://www.worldcat.org/search?q=isbn%3A0646387138"><em>Animal Breeding: Use of New Technologies</em> by Brian Kinghorn, Julius van der Werf and Margaret Ryan</a>.
(I highly recommend this book, but it's extremely hard to find a copy in this country.) (I highly recommend this book, but it's extremely hard to find a copy.)
I learned the truths that the sire rep and the BIF had been hiding (or ignorant of) the entire time. I learned the truths that the sire rep and the BIF had omitted the entire time.
It wasn't that mysterious of difficult, after all. It wasn't that mysterious or difficult, after all.
Most of the things that had been said were, in fact, lies, but only lies because they had been deprived of their mathematical context. Most of the things that had been said were, false, but only because they had been deprived of their mathematical context.
Knowing the truth became a whole new burden, though, as I became more angry every time I heard the half-truths and misunderstandings of the High Priests of Beef. Knowing the truth became a whole new burden, though, as I became more upset every time I heard someone abusing EPDs.
It was upon this sore toe and disgruntled spirit that the hammer of Mulliniks' ill-fated words fell. And one day I heard an academic who should have known better, and who had a great amount of sway among ranchers getting it blatantly wrong in a way that could directly hurt cow-calf producers.
As Marty Robbins put it, &quot;I couldn't stand no more.&quot; As <a href="https://youtu.be/YLgqgh7qAbU?t=116">Marty Robbins put it</a>, &quot;I couldn't stand no more.&quot;
</p> </p>
<h2>Something had to be done</h2> <h2>Something had to be done</h2>
<div class="row"> <div class="row">
@ -133,34 +151,85 @@ motto: Keep EPDs Real
<div class="col-md-9"> <div class="col-md-9">
<p> <p>
So I founded the #KeepEPDsReal movement. So I founded the #KeepEPDsReal movement.
The movement officially launched at the Albany County Fair 2019, where my colleagues and I wore and gave out buttons with the message MILK &ne; Milk. The movement officially launched at the Albany County Fair 2019
The premises of the movement are simple: <sup><a type="button" data-toggle="tooltip" rel="tooltip" data-placement="top" title="" data-original-title="I was originally going to get them printed and hand them out at an animal science conference that Mulliniks and I were both attending, but thought that might have been too harsh">*</a></sup>,
</p> where my colleagues and I wore and gave out buttons with the message MILK &ne; Milk.
<h3> I know that the message went over most people's heads, but there were a few that understood and heartily agreed.
Measure what you actually want to measure The premise of the movement is simple:
<br />
<small>MILK &ne; Milk</small>
</h3>
<p>
EPDs are useful tools to select for things that they actually measure, but if you try to use <code>MILK</code> to select for preg-rates or use <code>BW</code> to select for calving ease, then it's like you're using a wrench to pound nails with: you'll eventually get the job done, but it will take longer and the results might not be pretty.
The sire catalogs are riddled with these kinds of fake math, though.
Worse yet are the dollar-indexes that assume perfectly uniform conditions across the entire country all year long.
<a href="https://archive.org/details/animalbreedingpl032391mbp/page/n170">Selection indexes are important</a>,
but using them as the sole criteria for sire selection leads to <a href="https://archive.org/details/animalbreedingpl032391mbp/page/n164">genetic stagnation in the long term</a>.
And if you're assumptions are wrong going into a selection index system, then you're results will be flawed, too.
<a href="https://blog.steakgenomics.org/2018/12/bif-genetic-prediction-decision-support.html">Custom selection indexes</a> will never be a substitute for using the proper measurements at the proper time, either.
</p>
<h3>
Ranchers can do math, too
<br />
<small>Why doesn't everyone know <em>Y</em>=<em>Z&mu;</em>+<em>X&beta;</em>+<em>&epsilon;</em>?</small>
</h3>
<p>
EPDs are not hard to understand, and what with matrix algebra built into most scientific calculators, there is no technical reason ranchers shouldn't be taught how to create their own EPDs.
I'm convinced that as scientists, being open and transparent about the methods used to make EPDs will give producers more realistic expectations, wider acceptance, and lower skepticism of EPDs and genomic tools.
And I mean <strong>real</strong> transparency. Defining EPD by <a href="https://blog.steakgenomics.org/2019/03/epds-101-use-information-to-improve.html">reading the dictionary definitions of "Expected," "Progeny," and "Difference" and showing a bunch of pretty bell curves</a> doesn't cut it.
I'm trying my best to cover this point by publishing documents and computer programs for ranchers to calculate their own EPDs at <a href="https://github.com/millironx/beefblup">github.com/millironx/beefblup</a>, but I need help.
Like I said, I'm not an expert, so my programs and explanations are clunky at best.
</p> </p>
</div> </div>
</div> </div>
<h3>Ranchers can do math, too</h3>
<p>
EPDs are an excellent tool, and they aren't that hard to understand, but as long as sire reps, extension agents and professors continue to
shroud them in an air of infallibility, <a href="https://blog.steakgenomics.org/2019/02/epds-and-reasonable-expectations-in.html">people aren't going to trust EPDs</a>.
What with matrix algebra built into most scientific calculators, there is no technical reason ranchers shouldn't be taught how to create their own EPDs.
I'm convinced that as scientists (and engineers and statstitians and mathematicians), being open and transparent about the methods used to make EPDs will give producers more realistic expectations, wider acceptance, and lower skepticism of EPDs and genomic tools.
That means no more defining
<a href="https://blog.steakgenomics.org/2019/03/epds-101-use-information-to-improve.html">EPD by defining the individual words</a>,
and no more throwing around words like
<a href="https://blog.steakgenomics.org/2018/06/experiences-with-implementation-of.html">single-step BLUP without context</a>.
<br />
<small><em>Sorry, Dr. Decker, your blog was just too available and had all the key phrases: it was too hard to pass up.</em></small>
</p>
<p>
In addition to creating the buttons and this rant,
I have also created a <a href="https://github.com/millironx/beefblup">computer program for ranchers to be able to calculate their own EPDs</a>
and a corresponding <a href="https://github.com/MillironX/beefblup/wiki/How-does-beefblup-find-breeding-values%3F">help document on the statistics that make it work</a> using high school-level math.
With the creation of #KeepEPDsReal, maybe &mdash; just maybe &mdash; we can end all the misinformation surrounding EPDs and start using them to make
reliable breeding decisions that actually produce the desired outcomes of animal breeders across America.
</p>
<h2>Get Involved</h2>
<div class="row">
<div class="col-md-6">
<div class="panel panel-primary">
<div class="panel-heading">
<h4><i class="fas fa-medal"></i>&emsp;Get some buttons!</h4>
</div>
<div class="panel-body">
<p>
I have a stash of buttons that are crying out for people to wear them.
If you happen to run into me at something to do with livestock, I will likely have a few of them
and can give you some. If you are only acquainted with me through the Internet, you will have to
get your own buttons printed. Here's how:
</p>
<ol>
<li>
Download the button artwork:
<br />
<a href="/blob/Milk-is-Not-Milk.psd"><i class="fas fa-file-alt"></i>&emsp;MILK &NotEqual; Milk Button Artwork</a>
</li>
<li>
Order 1 &frac34;&quot; round buttons with the artwork on them.
<br />
I got mine from <a href="https://www.purebuttons.com/product/175-custom-buttons">Pure Buttons</a>, but you can get them anywhere that has the right size.
</li>
</ol>
</div>
</div>
</div>
<div class="col-md-6">
<div class="panel panel-primary">
<div class="panel-heading">
<h4><i class="fas fa-laptop-code"></i>&emsp;Write some code (or docs)</h4>
</div>
<div class="panel-body">
<p>
My vision is to have the <a href="https://github.com/millironx/beefblup">beefblup repository</a> become a full-fledged suite
of programs to calculate all kinds of EBVs with documentation that explains everything that's going on a a high school math level.
I would appreciate help through coding and pull requests on the git repo, from those who know more about EPDs than I do.
More details can be found there.
</p>
</div>
</div>
</div>
</div>
<p>
Through this movement, we hope to stop seeing the MILK EPD used for fertility and milk selection, docility treated as a &quot;quantitative&quot;
trait, economic indices used in zero-based profit calculations, and &mdash; well, you get the picture. Join me, and together let's <b>#KeepEPDsReal</b>!
</p>
<h5 class="float-right">&mdash; <em>Thomas Christensen</em></h5>
<br />

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