7/18/2008

VOX INTERPRETS NEW SCIENTIST

A while back, I had a spirited exchange with Vox Day, WND columnist and author of the popular Vox Populi blog.

Vox is an interesting character: an expatriate who lives in Italy, highly-educated and very opinionated. Most importantly, he tries to be fair, as in this recent post about the supposed eclipse of neo-Darwinism wherein he alludes to our past exchange.

First, a few clarifications for new readers: Vox refers to ND/TENS, which is his gloss for 'Neo-Darwinism/Theory of Evolution by Natural Selection.' The shorthand 'TENS' is actually of my own coinage from our previous exchange. Vox does not deny the present dominance and short-hand utility of TENS, but is highly skeptical of its future as a scientific theory because of what he feels are its predictive limitations. I've argued that while TENS does not make the sort of advanced detailed predictions one might expect from (say) Newtonian mechanics, it does provide an explanatory framework in which to make sense of many observations, and (more happily) a ready source of falsifiable hypotheses about the origin of these observations.

It should be noted that Vox's arguments are short on the sort of data that impress working biologists, but they are long on 'information + intelligence + pattern recognition.' But the question is, what if your intelligent attempts to recognize patterns are based on faulty information?

In this most recent post, Vox uses a copy of a New Scientist article which (frankly) sensationalizes some interesting findings in epigenetics to the point of distortion. But what can you expect? New Scientist is not peer-reviewed, and the author (Emma Young) is an Australian journalist with no science credentials who also writes juvenile sci-fi. I've got nothing against the latter, having fond memories of Heinlein's juveniles, but really this is a case of someone not knowing enough about the field looking to juice up a finding for a non-specialist audience.

And this is not an isolated case! Darwin's the biggest target there is within biology, and this is just the latest in a series of seemingly-annual pieces in the popular press that invoke some sort of 'revolution' that will somehow rewrite or overturn evolutionary biology. For example, consider PZ's response to the thunderous hype of Susan Mazur.

The fact is that the alternative inheritance mechanisms hinted at in Young's article (and they are far from being universally demonstrated) require a continuity of environmental circumstances from each generation to the next in order to be heritable---and what is that continuity of circumstances, if not natural selection? This is more of a conceptual problem for August Weissman than for Charles Darwin, who would've doubtless been quite excited, even pleased with these observations. In fact, if S.J. Gould were alive, he would probably be pretty quick to point out that these new observations would have fit in well with the pluralist nature of Darwin's thought, as he understood it.

Now, Vox, if you don't get the allusion to Weissman or Gould's pluralism immediately, let me humbly suggest that you need to drink more deeply of the Pierian spring which is evolutionary biology before presenting findings out-of-context on your blog. Next time, I'll explain why I disagree with Vox about the usefulness and appropriateness of terms like 'Neo-Darwinism.' I wouldn't be surprised if he didn't respond, so check out Vox's blog.

17 comments:

Ian H Spedding said...

Most importantly, he tries to be fair, as in this recent post about the supposed eclipse of neo-Darwinism wherein he alludes to our past exchange.

Fair?

...science marches on, and according to New Scientist, already appears to be on the verge of humiliating the Darwinian faithful who were foolish enough to insist, against both reason and the history of science, that ND-TENS is a solid and reliable scientific model in its current form:...

You have a curious notion of what it means to be fair.

But the likely question is whether Darwin will ultimately be regarded as more akin to Ptolemy or Newton, and in either case, his theories will almost surely not be revered as the secular scripture and basis for societal revisioning that they have been for the past 140 years.

Perhaps Beale believes an acid tone and withering contempt is being fair but others will see it differently.

What we see is a clever and well-educated man who chose to apply that intelligence to the fields of computer programming and video game design.

What we see is someone who believes that those skills, supplemented by reading some biology texts and journal articles qualify him as an expert critic of evolutionary biology, a position he shares with some of the denizens of Uncommon Descent.

What we see is someone who, rather than spending years studying the subject both at school and university leading to the actual practice of science both in the field and in the laboratory, prefers to snipe at those who have from the comfort of his armchair.

What we see is someone in whom the hostility towards evolution is rooted, not in the shortcomings of the theory itself, but in its perceived contradiction of his religious beliefs, again, a position shared with contributors to Uncommon Descent.

In fairness, I should, at this point, declare an interest or rather a bias. My experience of mathematics teachers at school was that they were arrogant, intolerant and contemptuous of those who did not find it as easy to grasp as they did. They left me with a deep and abiding loathing of both the subject and those who practice it. I see those same qualities in some of those who claim to speak for Christianity - or their version of it - here in the United States, so believe me when I tell you that, on both counts, whatever contempt Beale feels for evolutionary biology I return with interest.

In my own defence, I should say that I realise that such a view is neither rational nor fair. I am sure there are mathematicians who are kind, tolerant and will bend over backwards to be helpful to the more innumerate amongst us. I know, both from people I knew during my membership of the Church of England and from believers such as yourself that I have met since on the Internet, that there are still Christians who practice a faith which embodies the virtues of love, charity, compassion, tolerance and humility.

It's just a shame that the assholes get so much of the publicity rather than those who are more deserving of recognition.

Scott Hatfield . . . . said...

Hi, Ian!

You have a curious notion of what it means to be fair.

I was referring to the way that Vox, mindful of our previous debate, alluded deferentially to my views, in essence inviting me to reply.

As you noted, Vox is confident enough (perhaps arrogant?) to generalize from his past experience in other matters to conclude that he can draw conclusions about a field without really delving into its literature. My post essentially takes him to task by pointing out that he simply passed on someone else's misunderstanding of evolution.

As for Vox's motives, he is of course a Christian and politically conservative, but apparently has no problem with an old earth or natural selection per se. His real beef with biology as practiced is not so much the actual science (which he is smart enough to realize he doesn't know well enough to fence with) but with what he perceives as the metaphysical burden it is routinely used to justify. He walks an interesting tightrope between attempting to appease his conservative audience and being intellectually respectable. He has never once, for example, talked up ID or any other form of creationism even though many of his regular readers do. So, while I think he is boxing with shadows, I do think that by his lights he is trying to be fair.

wrf3 said...

An unrelated question, but I hope you can answer it. If DNA were to be likened to software by way of analogy, would it be data, data + code, or code?

windy said...

The fact is that the alternative inheritance mechanisms hinted at in Young's article (and they are far from being universally demonstrated) require a continuity of environmental circumstances from each generation to the next in order to be heritable---and what is that continuity of circumstances, if not natural selection?

You've got it backwards. Evolution requires inheritance. Inheritance is continuity of (internal) circumstances. Once there is inheritance, there can be evolution by natural selection or drift or both, regardless of whether that inheritance is genetic or epigenetic.

And I don't recall if someone pointed this out during your debate with Vox, but "theory of evolution by natural selection" is something of a misnomer when applied to modern evolutionary theory.

Scott Hatfield . . . . said...

Thanks for the comments and questions!

If DNA were to be likened to software by way of analogy, would it be data, data + code, or code?

The second, but it would be misleading to think that all of the data involved in an organism's development resides in the DNA.

You've got it backwards. Evolution requires inheritance. Inheritance is continuity of (internal) circumstances.

I think my sentence may be confusing, but not backwards. Yes, evolution requires inheritance of the replicating units within a population. But I was saying that the external circumstances, from the environment, is just another way of describing the action of natural selection, which serves as a filter ('Nature's broom') of genetic diversity. As Luther Burbank once said, 'Heredity is nothing but stored environment.'

Once there is inheritance, there can be evolution by natural selection or drift or both, regardless of whether that inheritance is genetic or epigenetic.

I agree. I'm sorry if my comment might have led you to believe otherwise.

And I don't recall if someone pointed this out during your debate with Vox, but "theory of evolution by natural selection" is something of a misnomer when applied to modern evolutionary theory.

Absolutely! But the point of using the gloss 'TENS' is to distinguish Darwin's mechanism for evolutionary change from evolution itself. We perpetuate a tradition of fuzzy thinking when we use the word 'evolution' (often capitalized) as synonymous with Darwin's thought, or with the action of natural selection. The point of 'TENS' is to have a quick, convenient way to make that distinction. To assert that this or that feature of any organism is adaptive, and could've been produced by the action of natural selection, in no way rules out drift or other mechanisms.

I have found that many creationists hold the beliefs they do precisely because they are unable to distinguish between concepts like speciation, natural selection and evolution. Once they are able to distinguish between them, they can see that all such concepts are (of course) facts and that what remains controversial is the relationship between the facts. Keep in mind, too, that if you don't make that distinction up-front, then later on the more sophisticated may realize something is amiss, that a word is being used in one sense in on place and in another sense elsewhere. They may understandably feel that they have been playing a 'shell game' with a dishonest opponent.

Narrowing the focus also allows us to distinguish between a theory which is known to be incomplete (TENS) and the modern synthesis, which is less so. By emphasizing the contingent nature of that synthesis, much of the opposition to considering the facts of evolutionary biology evaporate. This also helps us overcome the persistent but false meme that evolutionary biology (in Vox's words) is some sort of 'intellectual cult' held on faith.

windy said...

But I was saying that the external circumstances, from the environment, is just another way of describing the action of natural selection, which serves as a filter ('Nature's broom') of genetic diversity.

You did say that they "require a continuity of environmental circumstances from each generation to the next in order to be heritable", which implies that the environment somehow causes the inheritance. I know you meant external factors, but I disagree that a continuity of them is required for natural selection or inheritance (as an example, it is said that mammals still bear a "biochemical scar", a particular reaction to hydrogen sulfide due to past catastrophies:

http://seedmagazine.com/news/2008/04/suspending_life.php?page=all

As Luther Burbank once said, 'Heredity is nothing but stored environment.'

Yes, after natural selection has acted on it. And because neutral characters are inherited too, Luther was not quite right.

Absolutely! But the point of using the gloss 'TENS' is to distinguish Darwin's mechanism for evolutionary change from evolution itself.

Precisely. But I think you confuse them yourself, for instance you brought up the human chromosome fusion in a previous post and talked of predictions made by "TENS". But there is no need to assume that natural selection had anything to do with the fusion: the prediction was based on common descent.

Scott Hatfield . . . . said...

You did say that they "require a continuity of environmental circumstances from each generation to the next in order to be heritable", which implies that the environment somehow causes the inheritance.

For the special case (which is what Vox is hanging his hat on) in which some sort of external input from the environment influences what genes are inherited (as opposed to what is expressed), then I would say that an interaction between the environment and the genes leads to the inheritance pattern seen. My point was that if you required such an interaction in order to facilitate transmission of information at every generation, then this was just another special case of natural selection, and thus (as Dawkins says in the article) no problem for evolutionary theorists.

You must forgive me, because this is a special topic within epigenetics on which I am out of my depth. As I understand it, the special cases above are far from universally demonstrated!

Precisely. But I think you confuse them yourself, for instance you brought up the human chromosome fusion in a previous post and talked of predictions made by "TENS". But there is no need to assume that natural selection had anything to do with the fusion: the prediction was based on common descent.

That's an excellent point, and one of the things I hope to do THIS time when corresponding with Vox is pin him down on the question of common descent. And, of course, chromosomal fusion is a mechanism for the generation of genetic diversity, not a filtering mechanism like natural selection. However, consider: since natural selection requires such diversity in order to operate, it follows that any mechanism which has a reasonable chance of generating diversity is not only likely to occur, but to lead to heritable variations which will be selected for. And certainly no one would claim that the chromosomal fusion is inconsistent with any natural explanation! I spent so much time in the previous correspondence arguing with those for whom the converse is the default position that I lost my focus!

Well, I still have a lot to learn in communicating these ideas effectively to a potentially-hostile audience. Thanks for being a sounding board!

windy said...

For the special case (which is what Vox is hanging his hat on) in which some sort of external input from the environment influences what genes are inherited (as opposed to what is expressed)

Epigenetics does not influence which genes are inherited (that would be Lamarckism I guess), it's about heritable modifications to gene expression, as opposed to "regular" changes in gene expression. After the Abbie/PZ discussion there was some back and forth about the definition of epigenetics and it seemed that the line between epigenetic inheritance and all sorts of modifications to gene expression is getting blurrier.

That's an excellent point, and one of the things I hope to do THIS time when corresponding with Vox is pin him down on the question of common descent.

Are you going to restart your correspondence? I admire your tenacity at least ;)

PS: About Vox's supposed fairness: do you really suppose he's never heard Dawkins mention replicators before? He makes it sound as if Dawkins pulled the idea out of his ass as a response to these new results, when Dawkins' comment is perfectly in line with what he's been saying for decades.

Stan said...

ian sez,
"It's just a shame that the assholes get so much of the publicity rather than those who are more deserving of recognition."

From my perspective this applies directly to Dawkins, Hitchens, PZ and ilk. For example, Dawkins' memes (aka "ideas") should be ridiculed, not revered. Same goes for the magical "replicators" upon which common descent depends.

The utter disdain that is given non-believers of such fantasy is very much indicative of a cult of intellectualism, one which is accustomed to calling things "fact" when they are circumstantial; calling it "proof" when it is just a story.

Modern biology is in its infancy, changing over from an accounting system for living things, into an empirical science. Any "facts" determined empirically are conditional, and subject to modification: they are not Truth.

When evolution is used as Truth, it becomes very suspect indeed. This is the sociological factor that outsiders take into consideration, but that insiders seem not to understand... or maybe not care about.

It appears that even insiders can't really agree on definitions of terms. What does that say about agreement on mechanisms? To the outsider it suggests that the conclusion is sacred, the search for "supporting" data is on. In other words, it is being rationalized.

It's a "forest for the trees" thing.

Ian H Spedding said...

I was referring to the way that Vox, mindful of our previous debate, alluded deferentially to my views, in essence inviting me to reply.

Oh, I see! This is a special case of "fair". Oh, well, yes, in that case, I'd agree he was being very fair. :)

His real beef with biology as practiced is not so much the actual science (which he is smart enough to realize he doesn't know well enough to fence with) but with what he perceives as the metaphysical burden it is routinely used to justify.

So nothing really out-of-the-ordinary there, then?

He walks an interesting tightrope between attempting to appease his conservative audience and being intellectually respectable. He has never once, for example, talked up ID or any other form of creationism even though many of his regular readers do. So, while I think he is boxing with shadows, I do think that by his lights he is trying to be fair.

I respect your willingness to engage him in debate about his arguments without allowing his dogmatic and dismissive tone to rankle; and I can see that he perceives himself as some sort of freethinker whose sturdy independence finds expression in a refusal to align himself completely with any established line of thought. But doesn't that just make him a contrarian who would be best employed in The Argument Clinic?

Come to think of it, that applies to some others here as well.

Stan said...

"But doesn't that just make him a contrarian who would be best employed in The Argument Clinic?

Come to think of it, that applies to some others here as well."



Dismissive tone? Intent to rankle? Is that reserved for just yourself?

Ian H Spedding said...

Stan wrote:
From my perspective this applies directly to Dawkins, Hitchens, PZ and ilk. For example, Dawkins' memes (aka "ideas") should be ridiculed, not revered. Same goes for the magical "replicators" upon which common descent depends.

Popper recommended that scientists be bold in their conjectures. As far as I can see, that is all Dawkins was doing with his memes proposal. He wasn't offering it as some sort of revealed Truth handed down on tablets of stone - as is the wont of some other "ways of knowing" - he put the idea out there and has been largely content to let others run with it. Some have tried to develop it, others have treated it with the contempt you believe it so richly deserves. That's how science works

The utter disdain that is given non-believers of such fantasy is very much indicative of a cult of intellectualism, one which is accustomed to calling things "fact" when they are circumstantial; calling it "proof" when it is just a story.

Aren't these strawmen due for retirement soon?

Obviously I could be wrong but I seriously doubt if you will find any scientist who believes memes are factual in the sense that genes are. And although scientists are capable of talking loosely, if you pin them down they will be quite clear that "proof" only exists in formal systems like mathematics or logic. In science what counts is observation, data and explanation. If someone puts forward some speculative explanation of how life began, for example, it remains at best a working hypothesis until evidence comes in or a better idea comes along; which is also true, of course, of explanations such as a UID (Unspecified Intelligent Designer) - aka God - did it.

Modern biology is in its infancy, changing over from an accounting system for living things, into an empirical science. Any "facts" determined empirically are conditional, and subject to modification: they are not Truth.

I think it's pretty well established that there are living things on this planet and that they have changed over time, for example, so there are some facts there. As for the rest, I think it's fair to say that it's provisional and, no, it's not in any absolute sense "Truth"

When evolution is used as Truth, it becomes very suspect indeed.

Absolutely. And it is true of any other claim to possession of absolute Truth as well.

This is the sociological factor that outsiders take into consideration, but that insiders seem not to understand... or maybe not care about.

Scientists can be as blind as anyone else to the impression they give to onlookers but there is nothing wrong with that. Where they would be wrong is if, as you suggest, they create a false impression of knowledge or certainty or omniscience, either accidentally or deliberately, and do nothing about it.

It appears that even insiders can't really agree on definitions of terms. What does that say about agreement on mechanisms? To the outsider it suggests that the conclusion is sacred, the search for "supporting" data is on. In other words, it is being rationalized.

And what are scientists supposed to do about public misperceptions of the actual state of play in a particular field of research, especially if those misperceptions are being created or manipulated by opponents of science for their own religious and/or political ends - other than trying to present their own case, that is?

Unless you are arguing the post-modernist case that all accounts of reality are nothing more than socially-constructed narratives and there is no way to "privilege" one over the others, we are left with the position that of all possible accounts of reality some will be more accurate than others and that it is possible to determine empirically which they are and the extent of their correspondence with the reality they are attempting to describe and explain.

Scott Hatfield . . . . said...

It appears that even insiders can't really agree on definitions of terms. What does that say about agreement on mechanisms? To the outsider it suggests that the conclusion is sacred, the search for "supporting" data is on. In other words, it is being rationalized.

Oh, evolutionary biologists agree on the terms, Stan. Where we still tend to differ is the relative importance of this or that, and what (if anything) is required to more completely account for the fact of evolution. This confuses the layperson, regrettably, but these sort of arguments are the way that science is done.

If you doubt that, google any of the following terms/phrases to learn how evolutionary biology has survived past theoretical challenges:

'hopeful monster'

'orthogenesis'

'saltationist'

'mutationism'

'midwife toad'

'group selection'

'spandrels'

etc.

Stan said...

Well, Scott,
Actually it was you who refused for the longest time to accept the term "mutation". Perhaps you still do, I am not sure; however, every source you sent me to, and from which I returned the info to you, referred to "mutation with selection" as the cause of evolutionary diversity.

You told me that my 1998 reference was not up to date, yet you just referred to a 50 year old document the other day on my blog.

[Please see this site for interesting information on Modern Synthesis of mid-1900's vs neo-mutationism of more current eras]

The perception, I'm afraid, is definitely one of "pick and choose" that data which is favorable, ignore or reject that which is not. That is rationalization of a preconceived answer.

Ian wrote,

"I think it's pretty well established that there are living things on this planet and that they have changed over time, for example, so there are some facts there."

Actually the first part is fact, the second part is presumed, except in the (trivial) micro- case. If the second part were stated, "there were different living things at different times with an appearance of increased complexity and relatedness", then that would be an accurate statement of actual paleo-observations.

Relatedness is easily seen, proven and accepted; descent is not provable beyond speculation, including DNA speculation.

These errors of extrapolation might not be visible to the closely focused biologist, I am not sure. But they are suspicious to outsiders looking in, and cast doubt on processes within.

Also, if biologists are not claiming Truth for "evolution as settled science", they have a strange way of projecting it. The mouthpiece for such things is the ACLU, and certain science organizations which do in fact make such claims. Not refuting these Truth claims makes the entirety of the field suspect.

Stan said...

Dang, I didn't give the URL, here it is...

http://www3.interscience.wiley.com/journal/118634377/abstract?CRETRY=1&SRETRY=0

Stan

Scott Hatfield . . . . said...

Actually it was you who refused for the longest time to accept the term "mutation". Perhaps you still do, I am not sure; however, every source you sent me to, and from which I returned the info to you, referred to "mutation with selection" as the cause of evolutionary diversity.

Stan, that's just nonsense. I never refused to accept the term mutation. You are a one-note johnny on this topic, continually making an argument not with what evolutionary biology as it is, but with your misunderstanding of genetics. One more time: mutations come in a variety of types, some of which figure in evolution, others which do not. They are not the only sources of genetic variation, but to the extent that they are, they can be selected for or against based upon their phenotypic effects. There are other mechanisms that generate new combinations of genes, notably sex, and there are mechanisms (poorly-described as yet) outside of natural selection that can lead to wholesale genomic organization.

Relatedness is easily seen, proven and accepted; descent is not provable beyond speculation, including DNA speculation.

Stan, I can't prove that gravity operates in every corner of our present universe, because it's not all accessible to observation. But it is certainly parsimonious to infer that such is likely to be true, and terribly unhelpful to say, in effect, "Bah! I admit that gravity can be seen around here, but you have no 'proof' of its existence elsewhere!"

Absent evidence in favor of such a view, what would be the purpose in taking such a stance? How would it advance astronomy or cosmology to ignore the likely role of gravity in shaping the history of the universe?

In the same way, within biology the inference of common descent is the most parsimonious explanation for the independent convergence of separate lines of evidence, among them the fossil record, comparative anatomy, embryology, biogeography and molecular biology.

Unless you have empirical evidence that argues against common descent, what would be the purpose of taking such a stance? I can't speak to your motivations as well as you can, but I have a pretty good idea that you take this position to shore up your private religious views. Nothing wrong with that, but that isn't anything the scientific community can recognize as 'evidence', much less 'proof'.

Also, if biologists are not claiming Truth for "evolution as settled science", they have a strange way of projecting it. The mouthpiece for such things is the ACLU, and certain science organizations which do in fact make such claims.

I'm not in the truth business, and neither is the ACLU or the NCSE. Stan, you just admitted that evolution itself is a fact, so I assume that you think that is 'settled science.' Do you deny that natural selection has been observed to reshape populations genetically, even to the point of producing new species? That is pretty much 'settled science', as well. If the inference of past common descent is still but an inference, are you arguing that we should not teach the evidence that supports that inference? Surely homologous structures, biogeographic distributions, molecular homologies, embryological similarities, vestigial organs etc. are well-established facts!

If all of those are pretty much accepted (and they are), then what's your beef with? The ACLU or NCSE? Get real. These are not science organizations. They don't tell the scientific community what to research, nor do they get to dictate the state standards to the educational establishments. What they do is defend science education from illegal attempts on the part of sectarian groups to introduce creationism and other pseudoscience into the public school curriculum.

Listen! I work in the public schools. I see well-meaning (but typically misinformed) people who want to bring creationism into the classroom, all the time. I try to be nice to them, but some of the more passionate have to told, very firmly, that what they want to do is illegal and could subject teachers and schools to expensive legal action. I am very glad that NCSE exists, because if they didn't, I would have to joust with these folks on my own.

Nothing gets into the formal curriculum in the state I teach in (California) without being subject to an elaborate filtering process. There are national standards for teacher certification, state standards for curriculum and district standards for both curriculum and teacher evaluation. Do you honestly think that either the state or my district has any desire to wade into metaphysical territory, setting themselves up for a potential legal challenge? Again, get real. Ask yourself why virtually all of the legal actions are brought against creationists, rather than teachers like myself who teach the state standards.

Finally, it's kind of ridiculous for you to rub your engineer-trained hands together and cluck that we can't put past 'proof' of common descent on your precious present workbench, and so your skepticism is justified!

Engineering is an application of scientific findings, not science itself. Biologists do not commit 'errors of extrapolation' by using inferences, as long as they are well-supported by evidence and parsimonious with respect to the data available to us. We are well aware of the methodological problems caused by failing to meet those conditions, and so it comes across as ridiculously patronizing for a non-biologist with some scientific education to lecture us on some philosophical nicety. Get real. Our models, such as they are, will "succeed" or "fail" not on the basis of whether or not they satisfy your sense of what is appropriate or permissible as an engineer, but on whether or not they lead to testable hypotheses in biology.

Let me suggest to you that if you have an empirically-testable model which proposes something other than common descent for the diversity of life, then put it on the table for the scientific community to evaluate.

If all you have, though, is private reservations about where a naturalistic account of biological diversity might lead, then I have to ask: why should any scientist care?

emerod said...

It is quite fascinating to see an honest critique of the engineering perspective from a science teacher. It implies that biology should be taught as merely an abstract intellectual exercise, kind of like medieval theology.

I would suggest that any scientific model is a success or failure based on whether it has an engineering application. If it does not, it is merely a game of nomenclature and logic, suitable for children to play with until they find something useful to do.

I don't think that the average person is responsible for presenting an empirically testable model to the scientific community. Rather, the scientific community is responsible for presenting a relevant and useful model of reality to the broader society. To the extent it does not, it can be safely ignored by the average person.

That is not to say that scientists should not be allowed to play with their computer-generated models and their abstract notions of what may have happened at some unobserved time in the past. It is not necessary for science to completely agree with reality in order to build its theoretical constructs.

If all you have, though, is a theory about what a naturalistic account of biological diversity might look like, then I have to ask: Why should any non-scientist care?