# Introducing Jeffb

**URL:** <https://discourse.peacefulscience.org/t/introducing-jeffb/12570>\
**Category:** Conversation\
**Tags:** Introduction\
**Created:** [November 25, 2020, 7:11pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570 "2020-11-25T19:11:22Z")\
**Posts on this page:** 20\
**Page:** 5

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**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [December 19, 2020, 7:27pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/109 "2020-12-19T19:27:20Z")

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> [@jeffb](#):
>
> I really have to do that with Aron Ra (as you can imagine). My attitude is: despite his insults, I want to hear what he has to say.

If you want to learn about evolutionary theory, then you don’t need Aron Ra. There are many good study materials or even free online courses to help get you started.

> [@jeffb](#):
>
> So…again it’s been a while since I studied _phylogenies_ , but now might be a good time for review.

You could use Dr Ashley Carter’s video series on basic phylogenetics for this and if you still have queries, feel free to ask @John_Harshman.

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**Author:** ![Michael\_Okoko](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/michael_okoko/32/13148_2.png) [@Michael\_Okoko](https://discourse.peacefulscience.org/u/Michael_Okoko)\
**Post date:** [December 19, 2020, 7:42pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/111 "2020-12-19T19:42:30Z")

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> [@jeffb](#):
>
> But thankfully @swamidass jumped in. I’m certainly willing to listen to him (btw, apologies to the rest of you who, now that I recall I think might have been saying the same thing).

This reminds me of a friend whom I conversed with on evolution some time ago. He thought that evolution was inherently atheistic (probably got that from AIG, which paints it as such), until I dropped the bombshell that millions of Christians accept evolutionary theory worldwide. He was a bit surprised, and said he would look it up. We haven’t talked about it again, but it seems he might be willing to evaluate the evidence for evolutionary theory under the guidance of a fellow Christian than an atheist or agnostic scientist.

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 19, 2020, 11:28pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/112 "2020-12-19T23:28:12Z")

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> [@jeffb](#):
>
> Family comes in town tonight for the holidays…

You don’t think that’s a bad idea, under the circumstances?

> [@jeffb](#):
>
> But thankfully @swamidass jumped in. I’m certainly willing to listen to him

Why are you willing to listen to him but not to others? I hope it’s not just because he’s a fellow Christian. That shouldn’t be relevant.

> [@jeffb](#):
>
> I think I’ll try to take a little more time on these topics and but forth a better response.

That would be appreciated.

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**Author:** ![swamidass](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/swamidass/32/3_2.png) [@swamidass](https://discourse.peacefulscience.org/u/swamidass)\
**Post date:** [December 20, 2020, 12:20am UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/113 "2020-12-20T00:20:47Z")

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> [@John\_Harshman](#):
>
> > [@jeffb](#):
> >
> > But thankfully @swamidass jumped in. I’m certainly willing to listen to him
> 
> Why are you willing to listen to him but not to others? I hope it’s not just because he’s a fellow Christian. That shouldn’t be relevant.

Maybe because I’m giving him some space.

It’s overwhelming to have tons of technical posts disputing your ideas, with some of them rude. That isn’t an effective way for most people to come along.

Just take a slower pace, and be sure not too many people are engaging all at once.

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**Author:** ![Timothy\_Horton](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/timothy_horton/32/9410_2.png) [@Timothy\_Horton](https://discourse.peacefulscience.org/u/Timothy_Horton)\
**Post date:** [December 20, 2020, 12:36am UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/114 "2020-12-20T00:36:26Z")

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> [@swamidass](#):
>
> Maybe because I’m giving him some space.
> 
> It’s overwhelming to have tons of technical posts disputing your ideas, with some of them rude. That isn’t an effective way for most people to come along.
> 
> Just take a slower pace, and be sure not too many people are engaging all at once

How long is the proper time to allow a Creationist to post the same old tired YEC PRATTs before we’re allowed to ask questions or post rebuttal scientific facts? jeffb has told us he isn’t a rookie doing this but has been engaged in E/C discussions for years. What exactly is he being protected from?

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 20, 2020, 1:21am UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/115 "2020-12-20T01:21:33Z")

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> [@swamidass](#):
>
> Maybe because I’m giving him some space.

What constitutes “giving space” in this instance?

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**Author:** ![jeffb](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/jeffb/32/22795_2.png) [@jeffb](https://discourse.peacefulscience.org/u/jeffb)\
**Post date:** [December 20, 2020, 5:01am UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/116 "2020-12-20T05:01:49Z")

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> [@swamidass](#):
>
> > [@John\_Harshman](#):
> >
> > Why are you willing to listen to him but not to others? I hope it’s not just because he’s a fellow Christian. That shouldn’t be relevant.
> 
> Maybe because I’m giving him some space.
> 
> It’s overwhelming to have tons of technical posts disputing your ideas

Ok, I suppose I need to jump in here and _try_ to clear up some things.

First off @John_Harshman, I’ll have to apologize about the “willing to listen to him” comment. I see now it may have been taken as an insult. It wasn’t intended that way. If anything, it was this: Trust that was built.

To expound on that, and _since you asked_, I’ll give you the real reason I moved on: questionable motives and intent. That’s primarily it. The more the conversation went on, the less I trusted your motives, and therefore your credibility dropped, you obviously didn’t see me having any credibility, and the conversation was only going to get worse. I did us both a favor.

And after I moved on, I noticed someone who I knew didn’t have an ulterior motive (and therefore trusted) made a suggestion, which I decided to read. That’s really all it was.

BTW, Some ways to increase your credibility: Have enough confidence in evolution that you don’t _need_ to defend it. Have enough confidence in evolution that when an annoying new creationist shows up making his over-boastful claims, it doesn’t get to you. I really respect that kind of confidence.

**Moving on**  
@swamidass, I do appreciate you stepping in a bit. But I think all’s-good (well I do at least). There’s plenty of others here to dialog with, and plenty to chat about. In fact, he did bring up a good topic that I need to go re-address (phylogenies). As creationists, we have both biology and age to study, which hits _every_ field of science. It’s hard to develop expertise in all of them. I personally tried to get decent exposure to all the topics as I can. As for phylogenies, I now recall a bit more. I looked at it from both sides, but neither stood out ahead; and at some point moved on to other topics. Personally I didn’t see it ruling out design. I think it’s a challenging topic because we’re dealing with such a _large_ set of data that we’re trying to make a single conclusion on. I made a comment, likening it to “cloud-pondering”. That’s a comment I’d like to expound on at some point.

Well since you, and others seem to feel there’s a strong common-descent signal there, it’s worth a re-visit. And I do have one question about it, but that’s for later.

Plus, I _still_ haven’t posted the very question I came here to ask. And of course when I post that, that’s another thread I have to follow! PS can really pull you in, can’t it?? I think my wife is slightly annoyed at my latest ‘distraction’.  
Well…I hope that helps some. Family just arrived for the holidays, gotta go.

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**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [December 20, 2020, 5:13am UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/117 "2020-12-20T05:13:03Z")

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> [@jeffb](#):
>
> First off @John_Harshman, I’ll have to apologize about the “willing to listen to him” comment. I see now it may have been taken as an insult. It wasn’t intended that way. If anything, it was this: Trust that was built.

That’s gracious, but trust is not much of an issue if you examine the evidence for yourself.

> [@jeffb](#):
>
> It’s hard to develop expertise in all of them.

You don’t need much expertise. You just need to be willing to go to the evidence itself.

> [@jeffb](#):
>
> As for phylogenies, I now recall a bit more. I looked at it from both sides…

I’m not following your switch from the plural to the singular here. At what, specifically, did you look?

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**Author:** ![John\_Harshman](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/john_harshman/32/1121_2.png) [@John\_Harshman](https://discourse.peacefulscience.org/u/John_Harshman)\
**Post date:** [December 20, 2020, 5:33am UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/118 "2020-12-20T05:33:10Z")

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> [@jeffb](#):
>
> The more the conversation went on, the less I trusted your motives

I’m not clear why that would happen. Whatever do you think my motives are?

> [@jeffb](#):
>
> Have enough confidence in evolution that you don’t _need_ to defend it. Have enough confidence in evolution that when an annoying new creationist shows up making his over-boastful claims, it doesn’t get to you. I really respect that kind of confidence.

I don’t see that as a measure of confidence. If I see you making a grievous error of understanding, isn’t it a friendly thing to do to try to convince you of your error? I’m trying to present you with evidence, or at least to get to the point where you will examine evidence. I’m trying to find out what you know already, though generally not succeeding.

> [@jeffb](#):
>
> Personally I didn’t see it ruling out design.

That depends on what you mean by design. If you mean separate creation of kinds, I’m arguing for common descent. It’s impossible to rule out the possibility that God has influenced its course and impossible even to detect whether he has, assuming he’s being subtle about it. But he must be very subtle, as there are no smoking guns for design.

Before we can consider the evidence for common descent, we have to know what you think was separately created. Can you name some groups that you are sure are separate kinds? Bonus points if you can explain how you know. Are crocodylians all one kind? Birds? If either is not in your opinion, I can point you toward some data. Or if you don’t like that, how about primates?

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**Author:** ![RonSewell](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/ronsewell/32/6194_2.png) [@RonSewell](https://discourse.peacefulscience.org/u/RonSewell)\
**Post date:** [December 20, 2020, 6:08am UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/119 "2020-12-20T06:08:27Z")

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> [@jeffb](#):
>
> There’s plenty of others here to dialog with, and plenty to chat about.

Speaking of which…

> [@jeffb](#):
>
> I just started a TODO list, and put this on one there.

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**Author:** ![dga471](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dga471/32/5233_2.png) [@dga471](https://discourse.peacefulscience.org/u/dga471)\
**Post date:** [December 22, 2020, 4:49pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/120 "2020-12-22T16:49:00Z")

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Split this topic on December 22, 2020, 4:49pm UTC

22 posts were split to a new topic: [On Being Friendly to Newcomers](https://discourse.peacefulscience.org/t/on-being-friendly-to-newcomers/12846)

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**Author:** ![jeffb](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/jeffb/32/22795_2.png) [@jeffb](https://discourse.peacefulscience.org/u/jeffb)\
**Post date:** [December 20, 2020, 8:58pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/128 "2020-12-20T20:58:17Z")

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> [@John\_Harshman](#):
>
> > [@jeffb](#):
> >
> > The more the conversation went on, the less I trusted your motives
> 
> I’m not clear why that would happen. Whatever do you think my motives are?
> 
> > [@jeffb](#):
> >
> > Have enough confidence in evolution that you don’t _need_ to defend it. Have enough confidence in evolution that when an annoying new creationist shows up making his over-boastful claims, it doesn’t get to you. I really respect that kind of confidence.
> 
> I don’t see that as a measure of confidence. If I see you making a grievous error of understanding, isn’t it a friendly thing to do to try to convince you of your error? I’m trying to present you with evidence, or at least to get to the point where you will examine evidence. I’m trying to find out what you know already, though generally not succeeding.

Well I suppose that was yet another poorly worded post.  
So let me say this to everyone before I get too many replies:

I really did come here to learn, but I put myself in a poor position to. Apparently I’ve been away from the forum environment for too long, and had a poor start. Then I focused on someone else instead of my own mistakes: Coming in here too boastful, then put in a poorly worded post with too much into it (and not enough time to defend it). Can’t be surprised at the reaction I got.

Can you all do me favor and give me a re-start? There are a good number of people here I can learn from, but I need to position myself better to.

Plus I need to step away from PS for a bit, not only for family, but for my wife who is starting commented on my latest ‘distraction’ (PS).

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**Author:** ![Timothy\_Horton](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/timothy_horton/32/9410_2.png) [@Timothy\_Horton](https://discourse.peacefulscience.org/u/Timothy_Horton)\
**Post date:** [December 20, 2020, 9:02pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/130 "2020-12-20T21:02:18Z")

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> [@jeffb](#):
>
> Can you all do me favor and give me a re-start? There are a good number of people here I can learn from, but I need to position myself better to.

OK, fair enough. Consider this a reset. Also realize people being harsh on the **YEC ideas** you’re floating does not equate to personal attacks on **you**. Have a good Christmas if you’re not back in a week.

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<div class="post-metadata">

**Author:** ![Mercer](https://avatars.discourse-cdn.com/v4/letter/m/e274bd/32.png) [@Mercer](https://discourse.peacefulscience.org/u/Mercer)\
**Post date:** [December 20, 2020, 9:05pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/132 "2020-12-20T21:05:48Z")

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> [@jeffb](#):
>
> I really did come here to learn, but I put myself in a poor position to. Apparently I’ve been away from the forum environment for too long, and had a poor start. Then I focused on someone else instead of my own mistakes: Coming in here too boastful, then put in a poorly worded post with too much into it (and not enough time to defend it). Can’t be surprised at the reaction I got.
> 
> Can you all do me favor and give me a re-start? There are a good number of people here I can learn from, but I need to position myself better to.

Absolutely! I am impressed by your humility.

I would strongly suggest that when you do restart, you begin by keeping in mind the objective difference between evidence and hearsay. That is the key IMO.

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**Author:** ![dga471](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dga471/32/5233_2.png) [@dga471](https://discourse.peacefulscience.org/u/dga471)\
**Post date:** [December 20, 2020, 9:32pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/133 "2020-12-20T21:32:20Z")

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Split this topic on December 20, 2020, 9:32pm UTC

5 posts were split to a new topic: [Questions about forum norms](https://discourse.peacefulscience.org/t/questions-about-forum-norms/12832)

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**Author:** ![dga471](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dga471/32/5233_2.png) [@dga471](https://discourse.peacefulscience.org/u/dga471)\
**Post date:** [December 21, 2020, 6:12am UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/135 "2020-12-21T06:12:16Z")

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Split this topic on December 21, 2020, 6:12am UTC

10 posts were split to a new topic: [Evidence vs. Hearsay](https://discourse.peacefulscience.org/t/evidence-vs-hearsay/12838)

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<div class="post-metadata">

**Author:** ![dga471](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/dga471/32/5233_2.png) [@dga471](https://discourse.peacefulscience.org/u/dga471)\
**Post date:** [December 21, 2020, 6:12am UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/141 "2020-12-21T06:12:59Z")

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Split this topic on December 21, 2020, 6:12am UTC

6 posts were split to a new topic: [How to establish trust in a conversation](https://discourse.peacefulscience.org/t/how-to-establish-trust-in-a-conversation/12839)

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**Author:** ![T\_aquaticus](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/t_aquaticus/32/1249_2.png) [@T\_aquaticus](https://discourse.peacefulscience.org/u/T_aquaticus)\
**Post date:** [December 21, 2020, 3:49pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/143 "2020-12-21T15:49:06Z")

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> [@jeffb](#):
>
> So…again it’s been a while since I studied _phylogenies_ , but now might be a good time for review.
> 
> How does that sound? And btw, I hope there’s not a tight deadline on getting my homework in. Family comes in town tonight for the holidays…

Phylogenies are a perfect place to start.

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<div class="post-metadata">

**Author:** ![evograd](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/evograd/32/1233_2.png) [@evograd](https://discourse.peacefulscience.org/u/evograd)\
**Post date:** [December 22, 2020, 4:36pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/154 "2020-12-22T16:36:54Z")

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> [@jeffb](#):
>
> How can a phylogenetic tree be based on DNA evidence when some sequences have no match? One way is simply to ignore the orphan genes. In 2016 [three evolutionary biologists](https://www.ncbi.nlm.nih.gov/pubmed/?term=26549428) were able to construct a phylogenetic tree of insects only by ignoring 40 percent of the DNA sequences in fruit flies and 80 percent of the sequences in water fleas. Rather than strongly supporting the idea that all living things share a common ancestor, the DNA evidence has to be trimmed and crammed into the idea.

Nowhere in the paper do they say they were “only able” to construct the phylogenetic tree by removing those sequences. In fact quite the opposite, their figure 2 shows that even at very low cutoff values (including more sequences), they could achieve decent phylogenetic trees in comparison to the consensus tree. The cutoff they used was just the optimal value.

Removing orphans from the dataset is just removing uninformative data, not an attempt to cram the data to fit a phylogeny. As the authors say in the results and discussion:

> The protein numbers for the _e_ −75 cutoff range from 4000 to 5000 genes for _[Ixodes](https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/ixodes)_ and _[Daphnia](https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/daphnia)_ to 9000 for several taxa in the dataset. The concentration of small genomes in the basal taxa in the study is probably not correlated to any biological aspect of those organisms but rather to the inability of our method to establish orthology of many of the genes in these basal taxa. **Our approach eliminates any gene that is present in only a single taxon (such genes are phylogenetically uninformative).**

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**Author:** ![Rumraket](https://sea2.discourse-cdn.com/flex016/user_avatar/discourse.peacefulscience.org/rumraket/32/9328_2.png) [@Rumraket](https://discourse.peacefulscience.org/u/Rumraket)\
**Post date:** [December 22, 2020, 4:49pm UTC](https://discourse.peacefulscience.org/t/introducing-jeffb/12570/155 "2020-12-22T16:49:12Z")

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And in any case, two exactly matching pieces of text can be evidence of plagiarism even if the plagiarist only copied half the total text.

There is no logical error with inferring common descent from phylogenies of alignable DNA sequence even if not all the DNA sequence is alignable. It is of course logically unavoidable that when mutations accumulate in separate lineages that began identical, that they eventually look nothing alike.

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