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Challenge or Preserve the Paradigm?

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December 10, 2011 Tags: Science & Worldviews

Today's entry was written by Steven Benner. Please note the views expressed here are those of the author, not necessarily of The BioLogos Foundation. You can read more about what we believe here.

Challenge or Preserve the Paradigm?

This blog is the fourth entry in a series by Steven Benner (the first post can be found here). Throughout the series, Benner discusses the nature of scientific progress and the difficulty of defining what is and is not science. Discussion questions are included at the bottom of each post.

In my previous post, I argued that science is a thoroughly cultural activity, fraught with potential bias. The power of science, compared to other disciplines, consists of its ability to challenge paradigms while keeping the primary evidence in view.

In most fields of science, the person who sets up an experiment is generally the same person who analyzes its results. Thus, a part of the discipline of training scientists is to get them to understand and manage how they participate in a scientific enterprise that is their own. It is, we teach, not wrong that they have an interest in the outcome of an experiment. Indeed, it is impossible for them not to have an interest. What is wrong is not to acknowledge their own interest, and not to mitigate it using the processes particular for their field.

The processes are different for different fields. In medicine, we insist that pharmaceutical trials be done "double blind", with neither the patient nor the physician knowing who is receiving the drug and who is getting the placebo. In chemistry, we might run an experiment under a range of different, but carefully controlled conditions, something impossible when dealing with human patients.

But in any field, the most successful scientists establish within their laboratories a kind of dialectic. On Mondays, Wednesdays, and Fridays, we believe one thing. And act like we believe it. On Tuesdays, Thursdays, and Saturdays, we believe the opposite, and act like it. We might even cherry pick data to make the case "pro" on Mondays, just to see how strong that case is. But if we do, we make sure that on Tuesdays, we cherry pick data to support the "con". Operating throughout is the ability to do experiments, mix reagents, observe stars, or follow moose. These all give reality an opportunity to slap us in the face, to remind us to be not quite so certain that we know what we are doing.

Above all, we teach scientists to distrust all measurements, but to distrust most those that confirm what we want to believe. All experiments should be repeated to make certain that their results are reproducible, of course. But the experiments that are most in need of reproduction are those that produced data that support the proposition or theory that the student wants to support.

Scientists can also deliberately set goals to drive discovery. One way is through "synthesis", the act of creating something new following a design based on currently accepted theory. Synthesis has become especially big in biology, where "synthetic biologists" try to create new proteins, or new genetic systems, or new genetic regulatory networks based on what we think we know about living systems. If the theory guiding our design is correct, it should be empowering; the synthetic protein, the synthetic gene, or the synthetic regulators should work. But if the theory is wrong, it might not be empowering. The synthesis will then fail, and fail in a way that cannot be ignored. Thus synthesis drives discovery and paradigm-change in ways that analysis cannot.

But suppose scientists do not establish this kind of dialectic internally? Suppose the scientist, enamored with his innovation, simply becomes an advocate, publishing data to support the innovation while burying data that contradicts it, rationalizing away contradicting observations by introducing ad hoc explanations? In this case, the scientist has lost for himself the power of science to discern knowledge. His innovation must now be evaluated by the community.

Fortunately, the community of science offers the opportunity for correction. Unlike in the law, advertising, or politics, science does not have a jury, market, or voter who stands above the dispute, hears both sides, and makes an authoritative decision. Instead, there are rules that deny the existence of an authority. Data are made public. Experiments are open to be repeated in the laboratories who want to attack the innovation. New experiments are designed by others to test the innovation.

The interaction can be rough and tumble, with advocates on all sides showing little of the dispassionate disengagement of ideal scientists. Sometimes, the dispute is not resolved until the advocating scientists die, to be replaced by a new generation of scientists who can dispassionately evaluate the dispute. But as long as politicians do not intervene, science can be self-correcting.

In this activity, a community can easily become divided into warring parties of advocates. One of these disputes well known to biologists (but to few other communities of scientists) is the "neutralist-selectionist" dispute, which consumed a generation of evolutionary biologists arguing over whether or not most genetic change influenced the fitness (of a moose, for example).

A dispute well known to chemists (but to few other communities of scientists) is the "non-classical carbocation" dispute, which asked how bonds should be represented in organic molecules carrying a positive charge. Known to physicists (but to few other communities of scientists) is the dispute over the "Copenhagen interpretation", having to do with uncertainty and quantum mechanics. In each dispute, every observation presented by one side was immediately contradicted by data selected by the other. The debates were largely unresolved until the initiating protagonists had left the stage.

How should a community react when our paradigms are challenged? Certainly, we cannot drop everything every time some crackpot decides to challenge what he learned in middle school. Nor can we expect scientific communities, composed of individual humans, to be more liberal than other human communities, where a challenge to orthodoxy is generally met by a response equivalent to "kill the heretic".

But a scientist is not allowed to dismiss this challenge out of hand as ridiculous. Scientists need a process to balance the fact that settled science may be wrong against the need not to waste time with truly ignorant challenges to science.

The first element of this process is a familiarity with the "primary data", the actual observations that underlie the science that is being challenged. A good scientist is always able to answer the question: "So you believe that the Earth is 4.5 billion years old. What are the primary observations that support your belief?” Thus, when a paradigm is challenged, the disciplined scientist can say: "Well, let me see. Suppose our world view is wrong? What primary data must we have misunderstood? What else in our current view of reality would need to be revisited?"

For example, if someone challenges the current paradigm of by asserting that the Earth is not 4.5 billion years old, but rather was created by divine intervention 6000 years ago, the correct response is not: "You are crazy".

The correct response is: “Well, maybe. But if that is what happened, then much else of what we think we know must also be wrong. We will need a new explanation for how the Sun gets its energy, as our laws about nuclear physics must be wrong. As this is the physics that has manifestly empowered engineers to build nuclear power plants, we need to explain how they are doing so well even though they are operating with the incorrect laws. The same would go for the empowerment provided by science for the use of radioisotopes in medicine X-rays in dentistry.”

All of this empowering knowledge would vanish if the current paradigm concerning the age of the Earth were wrong. Ultimately, it is this interconnection between biology, physics and chemistry, the engineers who are empowered by their laws, and the breadth of observations that are accounted for by those laws, that constrain the search for paradigms in need of revision.

This search is on-going within all of these fields. Evolutionary theory as it is currently structured is not able to explain all of the puzzles that observations of natural biology present us. Physics as it is currently structured is not able to explain all of the puzzles presented by observation of the cosmos. Chemistry as it is currently structured is not able to explain all of the puzzles presented by observations of the molecular world.

It is entirely conceivable that paradigms within these disciplines are ripe for replacement. It is conceivable that the various received views will need dramatic revision. But these replacements and revisions will come from those who create dialectics within their own thinking, are fully conversant with primary data, and are prepared to revisit "settled science" whenever prudent as their views are challenged. Not from those who enter the debate as advocates.

In my final post in this series, I will argue that science is misunderstood by the lay public in large part because other voices in the public square hijack scientific imagery to take advantage of its status.

Discussion Questions: Dr. Benner describes the importance of primary data in determining when a challenge to an established paradigm might be legitimate. Do you think scientists do an adequate job of explaining the primary data behind their conclusions to one another? What about to non-scientists?


Steven Benner is a Distinguished Fellow of the Foundation for Applied Molecular Evolution in Gainesville, FL. He received his doctorate in chemistry from Harvard University. Benner and his group of researchers initiated synthetic biology as a field and invented dynamic combinatorial chemistry, which is currently being used in pharmaceutical development.

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HornSpiel - #66479

December 10th 2011

An interesting article that describes the processes and values that keep scientific knowledge from being biased. It clearly shows I think, why so may scientists would naturally tend to be skeptical of religion. In the first place they are trained to be skeptical. In the second, they will be particularly skeptical of any discipline that puts such stake in orthodoxy, the role of authority and tradition in validating knowledge, as religion does.

Can Christian theology benefit from the values of skepticism and testing that have proved so useful in the scientific world? If so how?


athanasius - #66481

December 10th 2011

Doubt has a very intimate relationship with faith so long as it searches freely. If it is met with reactions like “you’re crazy”, then no growth occurs. But when skepticism freely meets God in spite of itself, the experience is very powerful.


Jon Garvey - #66486

December 11th 2011

Hornspiel, theologians have been testing and skeptical for 2000 years. Remember Augustine, Athanasius, Abelard, Wyclif, Luther, etc, etc. If anything current academic theology is not skeptical enough of its own ruling paradigm, which is rational skepticism!

Even so, every good preacher preparing a passage of Scripture starts off by saying, “What does this actually say, as opposed to what I’ve always assumed it says?” Any educated person is trained to be skeptical - my beef is that scientists are sometimes so ignorant of other fields that they believe their own hype.


James R - #66482

December 10th 2011

Dr. Benner has given us an idealized portrayal of how the scientific community should behave when an orthodoxy is challenged.  And for the most part, I have no objection to his account.  The difficulty is that in many controversies the scientific community does not behave in the manner prescribed.

If we take two current examples, the debate over anthropogenic global warming (AGW), and over Darwinian evolution, we see this clearly.  (And to make sure I am not misunderstood, by AGW I am referring to the debate over the human component of global warming, not to any debate about whether or not the planet has actually warmed, and by Darwinian evolution, I am referring to the debate over the adequacy of random mutation plus natural selection as the primary evolutionary mechanism, not to any debate over whether evolution has even occurred.)

In both of these cases, many members of the scientific community (not just politicians and journalists purporting to speak for the scientific community, though there have been plenty of those) have behaved shamelessly and not at all in accord with the principles that Dr. Benner enunciates.

Criticism of AGW modelling, even responsible criticism coming from people with Ph.D.s from good universities and good publication records, has been angrily shouted down, often with the accompaniment of charges that the dissenters are deliberately misrepresenting the data because they are in the pay of the oil companies.  And of course critics have been called “deniers” (with the cultural associations of the phrase “he is in denial”) rather than critics, which is a rhetorical attempt to shift the argument from data and reasoning to motives.  Leading AGW proponents have mused privately in e-mails about how they might somehow shut down or at least shut out legitimate journals, staffed by Ph.D.s like themselves, which publish articles which do not agree with their views, and uncomfortable data points have been massaged to fit the prevailing theory, and not always with due notice to the public or to the government bodies which will be acting on policies based on AGW science.  And on the internet, some scientists have engaged in vile character assassination of opponents.

The same is true in the Darwinism debates.  Critics of neo-Darwinism, including many with Ph.D.s from good schools or positions at good universities, have been shouted down, abused, called “creationists” (even when some of them are agnostics and atheists), and attacked in all kinds of ad hominem ways, often with the tacit consent of the majority of biologists (who have not spoken up against these unscientific and polemical reactions).  Uncomfortable molecular data is ignored, or if noticed, not presented to the public or to granting agencies; demands for clearer explanations of evolutionary pathways have been angrily denounced as unreasonable; constant sermons are given on the need for “consensus science” and how everyone should go along with it; and scientists who are not even specialists in evolutionary biology, in some cases not even from the life sciences, have offered dogmatic and angry opinions in favor of the orthodox view based on hearsay or secondary literature, without reading the primary literature or doing any experiments or research in evolutionary biology themselves.      

I am not here arguing that AGW or neo-Darwinism are unsound theories.  I am arguing that some of their proponents have not behaved, when challenged by serious critics, in anything like the measured, rational, civilized way that Dr. Benner says that scientists generally act.  They have in many cases behaved defensively and even vindictively, defending their cherished views by any means fair or foul.

I hope that in his concluding column Dr. Benner will evaluate some of the material, especially blog material, put out by Ph.D.s in climatology and biology during these recent debates, and give his personal opinion as to whether the responses of “consensus science” to serious criticism have always been offered in the idealized manner that he presents.  I would like to think that he would be ashamed of at least some of the Ph.D.-holding, tenured members of his academic community, and that he would grant that, at least in some cases, the critics have shown more scientific responsibility than the defenders of the status quo.


HornSpiel - #66483

December 10th 2011

Jimpithicus (a.k.a. Jim Kidder) on his Blog  points to an interesting article about an example of the self-correcting nature of science.
Article  URL: http://arstechnica.com/science/news/2011/11/how-the-collapse-of-a-scientific-hypothesis-led-to-a-lawsuit-and-arrest.ars
Jimps blog: http://scienceandcreation.blogspot.com/2011/11/slightly-off-topic-why-science-works.html


Jon Garvey - #66485

December 11th 2011

It does seem that Dr Brenner writes on the sociology of science as a scientist rather than a sociologist. As a result, I agree with James R that the picture he presents is rather too rosy, or even self congratulatory. It is stripped of any real consideration of small complications like gaining or retaining tenure, funding, commercial interests, personal stakes in theories, etc. In other words, all the human issues that give science a sociological component at all. Consider this quote:

It is entirely conceivable that paradigms within these disciplines are
ripe for replacement. It is conceivable that the various received views
will need dramatic revision. But these replacements and revisions will
come from those who create dialectics within their own thinking, are
fully conversant with primary data, and are prepared to revisit “settled
science” whenever prudent as their views are challenged. Not from those
who enter the debate as advocates.


All this really says is that if some people discover the evidence that a ruling paradigm is wrong, and argue for it, face marginalisation, opposition or abuse (and all the stuff James R mentions) but eventually prevail, then it will be because they are self-critical scientists.

Well, yes, just as it was the self-critical theologian Martin Luther who fought all those battles to change the ruling paradigm of Catholic theology, the self-critical politician William Wilberforce who fought all those battles to replace the ruling paradigm of slavery… You’d expect science to be reformed by scientists rather than pop musicians or showjumpers, wouldn’t you? But that says nothing about how easy or difficult it will be to get others to take their evidence seriously since, by the nature of the case, it will be at odds with the ruling paradigm.

Take the example of the cortical inheritance work done from the 1930s to the 1950s on Paramecium by Tracy Sonneborn. In the genocentric atmosphere of the modern synthesis, what serious work has been done in the last 3/4 century to build on the research on this non-genetic mechanism of acquired change? If the 2011 conclusion is true that “the phenomena of cortical inheritance (and related nongenic, epigenetic
processes) remind us that the fundamental reproductive unit of life is
not a nucleic acid molecule, but the remarkably versatile, intact,
living cell,”
might it not have been useful for at least some people to have been chasing it up during the last 9 decades until the human genome project threw epigenetics into the spotlight? And is biology generally any less fixated on the genome even now?

Science is not unique in having tools for its own reformation, and neither does the history of science actually show it is vastly better than other human institutions at self-criticism. It’s not any worse, either, but the one thing that would make it so is a misguided belief in its own objectivity and rationality. Beware the people who say they welcome opposing opinions while they keep a firm grip on the reins of power.


Darrel Falk - #66487

December 11th 2011

James R (welcome back) and Jon,

Please note that Dr. Benner said this:
“The interaction can be rough and tumble, with advocates on all sides showing little of the dispassionate disengagement of ideal scientists. Sometimes, the dispute is not resolved until the advocating scientists die, to be replaced by a new generation of scientists who can dispassionately evaluate the dispute. But as long as politicians do not intervene, science can be self-correcting.”

He was primarily explaining “ideal science” and is fully aware, as we all are, that on the short term, science is anything but ideal and objective.  Ultimately, the pressures within the scientific community win out and in the process, something which moves us to a clearer understanding of truth prevails.  Note, however,  that he acknowledges that sometimes it doesn’t happen until members of the “old guard” die off.   Note also, that he stresses that for the process to work it must be set free, so much as possible, of political interference.  

I think you both are on the same page as him at the theoretical level. 

Jon Garvey - #66488

December 11th 2011

Fair do’s, Darrel! But my point is that it’s not only politicians’ interference that can maintain a paradigm beyond its usefulness, but a whole range of very human foibles.

Even Dr Benner’s “death/new generation” motif may be overly optimistic when one is dealing with a paradigm, or a metatheory, rather than the usual small scale theories. It would apply in biology, I guess, to things like adaptationism v. neutral theory, but how long would it take for a plausible, universal, but hard-to-define (and harder-to-test) assumption like “random with regard to fitness”  to be displaced, especially if an alternative implied an outlawed concept like teleology?

Tangential to this, but relevant to Dr Benner’s description of science’s modus operandi, I was intigued by this 1961 quote from historian of science W Cannon (Victorian Studies 5: 109-134):

Here I think we will eventually find the secret of Darwin’s
      greatness, in two traits not always praised in theories of ‘how to conduct
      yourself scientifically.’ One is Darwin’s notorious habit of jumping to
      conclusions without adequate evidence. He developed his coral reef theory,
      we remember, before examining coral reefs. The other is that of stubbornly
      maintaining his theories regardless of the valid arguments and evidence
      that could be brought against them. [Cannon’s note at this point refers
      the reader to the argument over the ‘Parallel Roads of Glen Roy’ paper.]
These are the procedures to be recommended, of course, only to the
      great; and I come to the regrettable conclusion that science takes great
      strides forward not primarily from laborious research, but rather when
      some biased person maintains his intuitions in public, and when, thereafter,
      generations of scientists find that some of these intuitions do actually
      illuminate whatever work they are doing.
   

That may be just observation or overly cynical, but it does ring true to what I observed over a career in my old field of medicine.


Darrel Falk - #66491

December 11th 2011

Jon said: 

”...my point is that it’s not only politicians’ interference that can maintain a paradigm beyond its usefulness, but a whole range of very human foibles.”

Jon, Don’t you think Dr. Benner has said as much?  My point in responding is to be sure readers as a whole are grasping the point he is making in the essay.  I think both you and James R are agreeing with him in theory.  See below for example:

“In this activity, a community can easily become divided into warring parties of advocates. One of these disputes well known to biologists (but to few other communities of scientists) is the “neutralist-selectionist” dispute, which consumed a generation of evolutionary biologists arguing over whether or not most genetic change influenced the fitness (of a moose, for example).

A dispute well known to chemists (but to few other communities of scientists) is the “non-classical carbocation” dispute, which asked how bonds should be represented in organic molecules carrying a positive charge. Known to physicists (but to few other communities of scientists) is the dispute over the “Copenhagen interpretation”, having to do with uncertainty and quantum mechanics. In each dispute, every observation presented by one side was immediately contradicted by data selected by the other. The debates were largely unresolved until the initiating protagonists had left the stage.


Roger A. Sawtelle - #66492

December 11th 2011

Please do not forget the dispute between James Lovelock and Richard Dawkins concerning the nature of biological change that continues today despite the success of ecological theory.


Jon Garvey - #66494

December 12th 2011

Darrell

Once more, I agree with you but with the reservation that (pending of course the next episodes) I don’t think Benner recognises (or shows he recognises) the degree to which science is no more privileged in self-correction than other fields. He says:

Fortunately, the community of science offers the opportunity for
correction. Unlike in the law, advertising, or politics, science does
not have a jury, market, or voter who stands above the dispute, hears
both sides, and makes an authoritative decision. Instead, there are
rules that deny the existence of an authority. Data are made public.
Experiments are open to be repeated in the laboratories who want to
attack the innovation. New experiments are designed by others to test
the innovation.

One could equally argue that in the law, the judiciary has full independence in legal decisions, whereas individual scientists have their faculties standing above the dispute (witness Sternberg) . More evenhandedly I’d say both professions have standards of independence, but equal dangers of worldview-bias, groupthink, political pressure and what have you.

If any of those are operating, the ability to repeat experiments or design refuting ones is a laborious option: it’s easier to bury the original research for a few decades, or say that “nobody” takes the work seriously (Margulis), or that the researcher is “heterodox” (Coyne on J Shapiro).

I don’t expect science to do better than other human disciplines, but it needs to be more aware that it doesn’t. To use quoted examples, the neutralist-selectionist debate appears as rancorous as ever, as does the Copenhagen interpretation. In both of these (to the confusion of the self-educator) the protagonists talk as if the debates were settled long ago in their favour. In the former case, neutralism seems to have won the day, yet in every debate natural selection is still trotted out as the universal acid of evolution.

Will we have to wait until all of us are dead, for example, for the science community to be saying consistently, “Dawkins’ selfish-gene concept was an intriguing 20th century approach, but bears little or no correspondence to reality”? Or will “Selfish Gene” still be used in schools forever?


Darrel Falk - #66500

December 12th 2011

Jon,


Benner is arguing that on the long term (decades) the culture of science is such that its internal forces—which require coherence with multiple sets of information coming from multiple lines of inquiry—lead us closer and closer to an understanding of mechanisms.  On the short term, there are all sorts of forces that interfere with this journey, but on the long term history shows that it works…and works remarkably well!!

I am sure you’re following along with our other series (“Monopolizing Knowledge”), which is running in parallel right now.  Here, Ian Hutchinson is showing that because science works so well, some in society tend to put science in a privileged position, such that knowledge is only true if it can be tested through the scientific process.  Science, they believe, is the great enticer, and all knowledge needs to be scrutinized under her lens and her lens alone. However, certain aspects of reality are not subject to the reproducibility criterion that drives the scientific process.  This does not make them less true or less real, but because of science’s success in some things, there is this tendency in society to consider her a sort of goddess for knowledge in general—for all knowledge—and thereby, in essence, to worship at her feet.

This is foolish.  Science only allows us to see a segment of reality.  Over the decades and centuries it shows us that segment with remarkable and absolutely beautiful clarity.   However, it only works when one can test for reproducibility. Where one can’t, science needs to move aside and let other means of understanding take center stage.

Jon Garvey - #66501

December 12th 2011

Darrell

Don’t get me wrong - I’m really pleased to see BioLogos talking at length about both the sociology and philosophy of science. Ultimately it’s my belief that both, and particularly the latter, are the root of most of what is controversial in the science-faith debate, so a good grounding in the issues is essential for “people of faith” (even Christians!) in science.

We need to understand better how approaches appropriate to one area can invade the other - in both directions, for scientism can infect faith just as fideism can infect science.

At the same time we need to beware the Gouldian non overlapping magisteria approach, because from the Logos viewpoint we believe that in the end there is one reality, which is God’s reality. If that’s the case, and if the overlap is rightly understood (which is where the proper area for debate lies!) then faith must lead to a distinctive approach to the pursuit of science, and better science will be the result.

As a “for instance”, we know how a convinced materialist like (say) Peter Atkins might pontificate on Christianity, and agree to disagree. But do we appreciate how his worldview might affect his science, and how a Christian might approach things differently? Or do we buy into a simplistic view that science itself is objective and unaffected by metaphysical presuppositions? All fruitful ground for examination, in my view.


Darrel Falk - #66503

December 12th 2011

Jon,


Good.   As I say we’re on the same page with regard to nature of science and its limitations.  For the next little while BioLogos is looking at this pretty carefully through the two other series running in parallel to this one by Benner.  Ian Hutchinson, in essence develops your point very nicely, I think.  But I also encourage everyone to follow the Dr. Rick Kennedy series, which—through the eyes of a historian who is quite knowledgeable about both theology and science—calls for a humility in what we know and how we come to know it.  It’s also a fun read.

HornSpiel - #66504

December 12th 2011

then faith must lead to a distinctive approach to the pursuit of science

The implications are enormous. What kind of faith do you mean? Does this mean that there would be different “sciences” for Hindus, Muslims, Christians, Jews and animists? Are you predicting the eventual dominance of the Christian worldview? Or do you think it does not really matter what kind of faith you have as long as you believe in a higher power that brings  order to the universe?

If science depended on “faith” then then object of the “faith” would become an axiom of science. This would resemble ore-enlightenment science? In those days there were different “sciences” in different religious area. In todays interconnected world that would mean competing sciences. The ID debate would pale in comparison.

I sympathize with your skepticism with  the Gouldian non overlapping magisteria approach, It implies that religious knowledge does not relate to the reality of the physical world. I certainly agree “there is one reality, which is God’s reality. ” There is, however an alternative to understanding the “overlap,namely complementarity. Science and religion, when rightly defined and understood, provide complementary insight into the same reality. When rightly understood the underlying heuristic of this approach, methodological naturalism, can be comfortably encompassed within  ones faith.
 
So let me propose an alternative to what you state above, which I hope we can both agree on:

then authentic faith will lead to an authentic understanding  of science, and better scientists (and science) will be the result.



Larry Rudd - #66507

December 12th 2011

I don’t mean to be a fly in the ointment but what is “authentic faith”? Wouldn’t this presuppose some kind of theology that was extensive enough to underpin ones worldview, with the incorporation of an interconnecting view of God, man and creation? For instance, taking one slice, a theological view of man is clearly applicable to this article. In Romans 1:18-22, Paul indicates (among other things) that those guilty of unbelief are guilty because they know the truth and suppress it. The only way we would know this to be true is to have it revealed from God. Why? Because in order to successfully suppress the truth from yourself, you must also successfully suppress the fact that you are engaging in this act of suppression. Scientists are not immune from this epistemological dynamic which colors their thinking and creates a presuppositional framework that they have to stay within to limit or direct their conclusions. If they are unbelievers, the Bible describes them as unregenerate or “dead in their trespasses and sins” (unless you’re a Pelagian . This successful act of suppressing truth about God to themselves, as well as their success at keeping their suppression from themselves, necessarily taints their view of anything that implies the truth of God as it relates to themselves and creation. Is everything they say wrong? No that’s not what I’m saying. What I am saying is that the worldview of an unbelieving scientist necessitates that any true idea about God they encounter must be changed in some way so as to not conflict with their successful act of suppression. This fundamental bias was not even eluded to in the article.


HornSpiel - #66511

December 12th 2011

Thanks for your response Rudy. You’re not at all a fly…

If I understand your comment:

To the extent that an atheistic scientist is in rebellion against God, I would agree with your conclusion. Yet I do not believe Paul was making a generalization In Romans 1 that applies to every unbeliever. Another biblical category are  seekers, such as the centurion who whom Peter was commanded to go, or some of the people that Paul spoke to in Act 17. For  seekers, which can certainly include some scientists, the study of the natural world can actually draw them to faith.

As to your question:

By authentic I essentially  mean correct. In other words, a correct interpretation of God’s written self-revelation will not conflict with a correct interpretation of what God has reveled in Creation. For example: Both are human endeavors, and so fraught with human weaknesses (Paul calls it the flesh). So among other things, authentic faith will produce humility in both theologians and scientists.


Larry Rudd - #66559

December 14th 2011

HornSpiel,
Geesh… I’m gone a couple of days and a forest fire starts. Anyway, in about 4 or 5 interchanges you declare that this horse has been beaten enough. I was hoping to respond before that happened, but I digress…

Paul was describing something profound. He was describing the basis for unbelief being a justifiable sin against God. Most importantly, that it isn’t a sin of ignorance. This epistemological description of unbelief is something very insightful. So insightful that it clearly points to an idea with an origin outside of us (see the self verification loop that I described previously). Such a comment coming from our Maker is highly plausible. Moreover, we could go in to numerous other verses describing the fall of man and then back that up with recorded history of the last couple of thousand years for empirical backup. Your lack of belief that Paul is not making a generalization about something that effects all of mankind is extremely weak.

My point is that everybody’s conclusion can be skewed because of unbelief and this necessarily applies to the unregenerate sinner who comes to draw a conclusion that entails the truth of or about God.

Per my theological bent, one must be regenerate prior to true repentance and belief. True repentance entails true belief. The only way to break out of this epistemological self-verification loop of unbelief that Paul describes is to be moved by something from the outside. That “mover” is God. Yes, I’m a Calvinist.

As for worldview…
It’s a interconnected web of presuppositions that inform our thinking. This will NECESSARILY influence the direction we take our thinking to draw a conclusion. Why? Because the most fundamental beliefs that create this interconnected web are not easily changed. We are very disinclined to change these beliefs because to change something we fundamentally presuppose will cascade outward to other presuppositions.

Short story…
Scientists are people, people are biased to keep the foundation of their worldview intact. Unbelievers, have a worldview that excludes truth of or about God via a persistent epistemological self-verification loop.

Shorter story…
All scientists are biased because they are human; unbelieving scientists are necessarily biased when it comes to conclusions that entail truth of or about God.

As for your answer about “authentic”...
Here’s your problem. An omniscient God condescends to reveal himself in written scriptures. This same God, created everything visible and invisible that we can perceive and continually controls it. He changes hearts, He reveals things, His will is done.

You said, regarding the interpretation of God’s written revelation: “will not conflict with a correct interpretation of what God has reveled in Creation.” This presupposes an omniscience on man’s part regarding creation that doesn’t exist. Not only that, it denies the reality of the bias I previously described. Especially, when take as “gospel truth”, the conclusions about God’s creation presented by unbelievers?

There is a justifiable reason for skepticism when an unbeliever draws a conclusion about creation that excludes its Creator. Not that it should be disregarded out-of-hand but accepting conclusions without some theologically motivated skepticism is inconsistent with reality.


Jon Garvey - #66513

December 13th 2011

Hornspiel

Cans of worms indeed! But I’d argue that the worms are crawling about anyway, but are largely invisible partly because the consensus in science is to subordinate the search for truth to a unified metaphysical approach and an illusion of objectivity (“we don’t habe a drugs problem in Essex…”).

It’s not that there ought to be Muslim, Zoroastrian, atheist views of science - it’s that there will be if people of those worldviews are in science. After all, if a worldview doesn’t affect your view of the world, what is it?

Take the old example of Kepler - convinced that a rational God must have created an orderly cosmos, beavering away at the maths and Brahe’s observations until the sums worked (and spattering his notes with devotional comments!). If his worldview had been comfortable with happy accidents that  “sort of” worked the science would have been different - indeed it was, till he changed it. A parallel might be the concept of “bad design” in evolution - a biological Kepler would have looked for an explanation because “God ultimately did it, and he doesn’t do bad design.” A materialist would have expected chaos anyway and moved on.

Is such diversity a science-destroying problem? In that it exposes the myth of scientific objectivity, yes. But in practice, a disclaimer at the end of the paper “I bring a process view of theology / a materialist metaphysic / a Neoplatonic philosophy  to my work,” would enable one to assess whether the science was being informed or abused by the worldview.

As things stand, as the ID debate shows, metaphysical commitment is something many scientists expose as if it were a secret vice, whilst openly espousing materialism as if it weren’t such a commitment. That’s why a paradigm shift is needed. There is still too much of the same kind of naive attitude that some rationalist shouted at me in Trafalgar Square in 1971: “I am objective! YOU are subjective!”

The question you ask about the predominance of a Christian view is separate. Unless one believes in the bogeyman of a Fundamentalist Theocracy it’s likely that people’s diverse worldviews will continue to reflect whatever is happening in society and their personal lives. On the other hand, if one worldview is closer to the truth than another, one might expect it to show in the progress of science - do agnostics predict findings overall better than Baptists, or vice versa? Were teleology to become incontrovertible from the evidence, atheists would still create epicycles to deny it, but there would be fewer of them.


HornSpiel - #66525

December 13th 2011

Jon,

I’m afraid you are conflating faith with worldview. Christians can have different worldviews and people of different faiths can share he same worldview. Having grown up in the US in the 60s, I share a worldview much loser to by childhood best friend, who is Jewish, than I do with my brothers and sisters in Christ who grew up in Cameroon (where I lived for a while) in an animistic cultural milieu. Some even argue that the African worldview, which takes the pervasive influence of the supernatural realm for granted, is much closer to the Biblical world view. I have been told stories about people’s out of body experiences that absolutely stretched my concept of reality. But even a couple of nights ago, I heard reports of people seeing and hearing angels singing during the presentation of our church’s Christmas musical.

But do those subjective experiences have any relevance to science? Would it be profitable to create departments of angelology and astralprojection on the basis of such reports alone? No. Only if those phenomenon can be detected and measured by outside observers. Only when objective data is recorded and made available to others for evaluation do we have science.

As Christians we believe that God’s handiwork is reflected in the physical universe. I think we might also agree that natural laws and processes fit into our faith as the orderly way God consistently works to sustain the universe. That, I maintain is the limited realm of science.

What ID claims is that there are anomalies, inconstant with any conceivable natural law, that require the intervention of a designer to explain. ID advocates argue that those too should come withing the purview of science. I would agree with them if evidence could be amassed that point to such interventions as a normal, predictable, and measurable pattern within nature.

To get back to the question at hand. Although one’s faith and worldview do color our interpretations of scientific findings, and even what avenues a scientist might want to pursue, I do not think that faith  or worldview ultimately should have a place in scientific theories. As I mention above, science is about what the community of science can observe and measure and make predictions about—God’s normal consistent way of sustaining the universe.

To put it in a Christian context: Science is about describing God’s general revelation, available to all people regardless of their worldview or faith commitment. If people see God in it, then great. But for the most part they will not, unless they already have a faith commitment (Romans 1:18ff). In other words, the Bible teaches that the perception of the Creator is in Creation does not come simply by studying nature (science), but by being open to a greater truth.


Jon Garvey - #66531

December 13th 2011

Hornspiel

I used “worldview” advisedly, but you’re right that worldview is largely a matter of national culture. Nevertheless, there is a fundamental difference in worldview between atheist materialism and Christian teleology. Indeed, the call of Christ to be “in the world but not of it” is a call to reshape ones worldview.

Your astral projection science is a straw man, because there is no reason why a scientist of whatever persuasion would cease to investigate the natural world and try to do science on the miraculous, knowing it to be non-reproduceable. Nobody’s suggesting mullahs doing the lab-work. Materialists do, nevertheless, sometimes study the supernatural in an attempt to reduce the miraculous to the natural, which is curious.

“What ID claims is that there are anomalies, inconstant with any
conceivable natural law, that require the intervention of a designer to
explain.” No it doesn’t, really. It claims specified information is present and susceptible to detection, which is as consistent with natural law as all other information, and which requires a design explanation, though not necessarily with any more “intervention” than the design of the Universe itself. Negatively, they claim that the degree to which events are currently attributed to “chance” is inconsistent with any conceivable natural law - that’s an evidential matter and deserving of dispassionate investigation.

I agree with you completely that faith or worldview should not have a place in scientific theories, which of course includes talking about “undirected processes” etc. However, they will, as a matter of sociological fact, actually underlie the questions scientists ask and the interpretations they put on data. Therefore those worldview commitments should be acknowledged openly, rather than wished away by a self-delusion of objectivity.

I’d agree with your words on the limitations of general revelation, but I actually think that the vast majority of ordinary people do see God in the works of nature, if they do not receive a strongly metaphysical counter-narrative at the same time. Job’s narrative of “he provides the lion and her cubs with her prey” differs markedly from “evolution has made the lion a pitiless killing machine.” Naturalists without a sound-track to listen to have come to either conclusion, but most of us get our meta-narrative from education and the media.


HornSpiel - #66548

December 13th 2011

I think we have beat this horse enough here.

Just a few points of clarification. When you say:” [ID] claims specified information is present and susceptible to
detection, which is as consistent with natural law as all other
information, and which requires a design explanation,” I assume you say “require” because it is claimed that the probability is too low for it to have occurred otherwise. Also did you say elsewhere ( or  do you believe) that there is a difference between “design” and “manufacture?” That the design in nature we see could have been maufactured by the natural processes  currently attributed to evolution? If so, does ID science wants to replace the current concept of evolution with something more like an unfolding?


James R - #66552

December 13th 2011

Hornspiel:

If I may jump in on this discussion with Jon, I would like to congratulate you on your reasoning in the last five lines.  Yes, at least some design theorists do see evolution as an unfolding.  See, for example, Nature’s Destiny by Michael Denton (a book praised by another design theorist, Michael Behe). 


Jon Garvey - #66577

December 15th 2011

Sorry for delay, Hornspiel - been away for a day or two.

Q1:  I assume you say “require” because it is claimed that the probability is too low for it to have occurred otherwise.

Almost - to nuance it more, I’d say a design explanation simply requires design. What hits the probabilities are illusory features of design, which need to be achieved by even partly random processes.

Expansion on that: the crude probability of the letters of this post is 26^n where n=letter count, which tells you it’s not likely to be a repetitive, law-produced pattern. Since it makes sense to you, its appearance here by random electronic malfunction at such odds is completely infeasible. But since you were expecting someone like me to produce something like this as a reply, probabilities don’t have much to do with it. It’s all too predictable!

So wrt, say, random mutation, the appearance of a complex functional protein must either be
(a) the lawful result of completely unknown chemistry (which its complexity militates against), or something similar like functional proteins happening to be close together in the search space, quadrillions of similar-length proteins having the same function, etc. Both are suggested, but poorly supported.
(b) A randomly produced phenomenon (which its functionality and its high complexity militates against).
(c) A designed phenomenon, which matches its complexity and its functionality
.
Note that the “Mount Improbable” chance + NS solution, of allowing short steps, is akin to saying it’s easier to win £1m on the lottery with 10,000 consecutive £100 wins than with a single jackpot. NS throws away stuff: it doesn’t find it.

Q2:  Also did you say elsewhere ( or  do you believe) that there is a
difference between “design” and “manufacture?” That the design in nature
we see could have been maufactured by the natural processes  currently
attributed to evolution? If so, does ID science wants to replace the
current concept of evolution with something more like an unfolding?

“Design” and “manufacture” might both be poor descriptions in the sense of appearing too mechanistic. But ID people have done some careful work on defining “design” from the standpoint of detection. That doesn’t imply that other things aren’t designed, nor even that design, in the restricted sense, covers the whole creative process. Similarly as I understand it ID isn’t attempting to pin down a “manufacture” model:
(a) Because if it’s right about the inadequacy of the data to support Neodarwinian evolution, it’s also probably too poor to validate any other specific process as yet,
(b) Because a designer could in principle introduce detectable design at any level from controlling quantum or stochastic events to hey-presto miracle. With my Calvinist TE hat on this will do nicely: God controls chance, so that the arrow shot “at a venture” hits the disguised king as per God’s prior prophecy. But note the “design” features in that instance - as a random probability it’s vanishingly unlikely, though less so than a protein-chain.
(c) Because in the current state of play there’s no consensus. I doubt any of the the ID boys  would argue much with any natural process, including robust models of evolution, that revealed the mechanics: because design would still be there, just as it in this post whether I typed it, dictated it, or got my brother to ghost it for me.


James R - #66533

December 13th 2011

HornSpiel:

The term “worldview” is used loosely, and in different ways by different people.  It is unclear to me how you are using it here.  You seem to mean something like “general ideas about what sort of things exist in the world,” and you seem to think that these general ideas are shaped by culture rather than faith.

I would agree that our general ideas are heavily shaped by our culture.  But they are also heavily shaped by faith.  Even your own example of “animism” in Africa shows this.  “Animism” is not something specific to the culture of Cameroon; it is found elsewhere in Africa and elsewhere in the world, and in ancient times was very widespread.  You can call it a world view if you like, but it is also an aspect of a particular religious faith, a faith in unseen personalities or quasi-personalities which pervade nature.  An animist looks at the world in a way different from the theist, and that difference is theological as much as cultural, in fact, more theological than cultural.  An animist also looks at the world in a way different from the atheist, which is why (as you rightly say) the animist is in some ways more open to the teaching of the Bible than the atheist (or Protestant cessationist) is.  World view is connected with religious faith—with the sort of God or gods in which you place your ultimate trust.

I don’t think Jon or anyone else is saying that we should change the way we do science by directly importing notions from particular religious traditions, e.g., by postulating the influences of good or evil spirits on planetary motion.  I think he is saying that in fact our world view and our faith (which often overlap in various ways) influence the way we do everything, including science, and that therefore we should be conscious of that influence, and honest about it.

In Provine’s famous statement about not letting a Divine Foot in the door, you see how scientific methodology is directly determined by a materialistic world view.  But at least Provine is conscious and honest that he allows his world view such sway over his science.  Not all scientists, not even all Christian scientists, are so conscious or honest.

Yes, natural laws and processes do fit into Christian faith.  But so do interruptions of those laws and processes.  Indeed, to an unprejudiced reader of the Bible, i.e., to one who is not blinkered by a very modern “world view” (to use your term), the interruptions of those laws and processes are quite as important a part of faith as the regularities (even though they are understood to happen far less often).  I find that many Christians, including TEs, tend to miss this.  Of course I am not saying that the miraculous should figure directly into particular scientific hypotheses.  But its central role in Christian faith should make Christian scientists humble about the possible limitations of naturalistic explanation.

Two side points:  (1) ID does not require the assumption of “supernatural intervention” in order to draw its inferences; (2) Romans 1 does not teach that a “faith commitment” is necessary for human beings to recognize the order of the cosmos—quite the opposite.  (See also Psalm 19.)  Of course, a believer might see more deeply into nature than an unbeliever, but the unbeliever can see enough to be “without excuse.”


James R - #66539

December 13th 2011

Hornspiel:

Correction to my post above:  where I wrote “Provine” I should have written “Lewontin.”


HornSpiel - #66550

December 13th 2011

Jon and James,

Why do you avoid my main point?  Namely, science is about observing and measuring and in order to make predictions (theories) about what will happen in the future if such and such happens or if we do such and such, and secondly to explain the past. Perhaps it would be profitable to continue the discussion in the current blog post: Monopolizing Knowledge, Part 2: Reproducibility


James R - #66551

December 13th 2011

HornSpiel:

I wasn’t trying to avoid anything.  You made some comments about “world view” and I responded to them, hopefully intelligently and usefully.  I am sorry if I bored you, but I thought the topic of world views was of interest to you.

As for what science is, yes it involves all the things that you say above, but pay particular attention to the last one:  “to explain the past.”  Most of the heated arguments in the science/religion areas are not about observing and measuring and making predictions about the future.  They are about origins, i.e., about explaining the past, as you put it.  Now if it turns out to be necessary to include design as one causal factor in order to explain the past, what is wrong with that? 


Jon Garvey - #66578

December 15th 2011

I wasn’t trying to evade it either - it’s just a truism. And equally true whether your metaphysic is naturalistic or theistic… except that  the former will restrict your ability to deal with all eventualities (see Alvin Plantinga on methodological naturalism here - he has a new book out on science/religion - I hope it’s reviewd here sometime!)


Jon Garvey - #66583

December 15th 2011

Hornspiel: useful link to an essay by Plantinga. I find he thought of what I’ve been saying first!
http://www.arn.org/docs/odesign/od181/methnat181.htm


HornSpiel - #66592

December 15th 2011

Thanks for the link.



I am puzzled though by Plantinga’s thesis
that “in many areas, science
is anything but religiously neutral.” What his examples describe are
scientists, not science, not being religiously neutral. The scientific
findings he cites as being twisted to promote or justify atheism
(altruism, evolution, and fine tuning) can be, in the hands of a
believing scientist, arguments for just the opposite. Supporting the
idea that science, properly understood, is neutral.


Jon Garvey - #66608

December 16th 2011

I think Plantinga addresses the inevitability of bringing ideology into ones science later in the essay (maybe in part 2 if memory serves). Part of his point is that these non-neutral scientists are able to get their stuff published by the broader community as science, whereas a theistic scientist arguing for Mother Theresa’s actions being a result of Divine grace (for example) would not.

Plantinga’s not a lightweight, and even his opponents recognise him as one of the great living philosophers of science, so it pays to engage fully with his arguments. He’s a Christian, too, so I’m surprised his name comes up so seldom at BioLogos.

The whole point, I think, is that “science properly understood” is a construction that ignores the inevitable human realities - pretty much the thrust of my whole contribution to this thread. Compare:
“Christianity properly understood leads to a perfect society.”
“Government properly understood always seeks the greatest good for all the people.”
“Journalism properly understood is unbiased, truthful and educational.”

All those things are true, but everybody recognises that they remain exhaustively true just as long as they’re not practised by real people.

In science education, is it better to teach kids an idealised view of science that doesn’t exist in real laboratories, or to show them how to recognise their own ideological biases, control them and even use them productively to do better science?


beaglelady - #66524

December 13th 2011


Take the old example of Kepler - convinced that a rational God must
have created an orderly cosmos, beavering away at the maths and Brahe’s
observations until the sums worked (and spattering his notes with
devotional comments!). If his worldview had been comfortable with happy
accidents that  “sort of” worked the science would have been different -
indeed it was, till he changed it. 



But should scientists start investigations with a hard and fast conclusion of what they will find? What would Kepler think about colliding galaxies, asteroid strikes, and the like?
 

In the words of Neil deGrasse Tyson,

“And as our ordinary, optical telescopes got bigger and better, more
mayhem emerged: galaxies that collide and cannibalize each other,
explosions of supermassive stars, chaotic stellar and planetary orbits. 

Our own cosmic neighborhood—the inner solar system—turned out to be a
shooting gallery, full of rogue asteroids and comets that collide with
planets from time to time. Occasionally they’ve even wiped out
stupendous masses of Earth’s flora and fauna. The evidence all points to
the fact that we occupy not a well-mannered clockwork universe, but a
destructive, violent, and hostile zoo.”





Jon Garvey - #66526

December 13th 2011

Hi Beaglelady

Whether or not scientists should start out with presuppositions (Kepler’s weren’t of what he would find, but that he would find something consistent with God’s rationality), the fact is that it was following those presuppositions for a lifetime that in practice solved the problem that had exercised astronomers since classical times. And his conclusions still hold good for the cosmos we observe, at least at Newtonian scales.

Which is the argument from success that, if I remember, Dr Benner used in his first article.

On the matter of violent events, Kepler would have had no problem - it was the highly visible supernova of 1572 that had already swept away the Aristotelian idea of the changelessness of the heavens and paved the way for his work.

Your quote from Tyson - “a destructive, violent and hostile zoo” etc - is one example of what I mean by a worldview being allowed to impose on science. Kepler was well aware that destructive forces exist in the Universe, since he was largely blind from a childhood illness, but clearly chose to interpret that in a Christian way (and keep it out of his science, I suspect). If Tyson was purporting to write about science, he had no business talking about galaxies “cannibalising”, “chaotic orbits” (when he simply means “irregular”), “well mannered” universes or “hostile zoos.” Unless, that is, he has data on the ethical motivation of astronomical bodies that he hasn’t published in an astrology journal yet.


beaglelady - #66530

December 13th 2011

Even if we attempt to control Tyson’s writing,  he still notes events that are far from orderly.  


Jon Garvey - #66532

December 13th 2011

“Orderly” by whose judgement? Do they disobey the laws of physics? Are they any more destructive than the forces people have experienced from earthquakes, floods and disease since humanity existed, and usually fitted comfortably into a theistic cosmology?

I’d never want to control anyone’s writing - but I would want to distinguish science writing from purely emotive polemic.


beaglelady - #66541

December 13th 2011

You are the one who said that Kepler was  convinced that a rational God must have created an orderly cosmos.   And I’m pointing out that it isn’t exactly orderly, as that word is normally used.  An asteroid strike is no more orderly than the tsunami it will cause if it hits the ocean.  Heck, there was even a planetarium show called “Cosmic Collisions.” 


James R - #66545

December 13th 2011

beaglelady:

I have no idea whether or not you have any formal training in science, but based on your remarks to Jon, you appear to be unaware that when an asteroid violently strikes the earth, it is following the same laws of nature that obtain when the moon peacefully circles the earth.  And the tsunami caused by the asteroid strike will also follow those same laws.  The orderliness of nature is preserved in all cases.  The only difference is that certain results (i.e., certain contingent events) produced by that orderliness are less pleasant than others as far as human beings are concerned.  That hardly counts against the existence of a rational God, as any careful reader of Job understands.

I fail to see the relevance of the fact that you have seen or heard about a planetarium show.  And you appear not to distinguish between what a scientist like Tyson does when he writes in professional journals and what he does when writes for the general public.  Based on your quotation, when he writes for the general public he allows himself sloppy, emotional, and misleading statements that he would never put into a scientific journal article.  I simply disregard scientists when they write in this manner.  If I want rhetorical writing about nature I can read a novelist or poet. 


beaglelady - #66547

December 13th 2011

Why has the conversation now shifted to the laws of physics?  I never mentioned the laws of physics and in no way implied that an asteroid strike would violate them. 



Gee, first we find out that a wobbly planet wouldn’t be part of an
orderly universe, and suddenly the topic is the laws of physics.


(btw, the earth really does wobble on its axis!)


Jon Garvey - #66579

December 15th 2011

Beaglelady - a repeat apology for delay: I’ve been away.

Not only Kepler, but all the ancient natural philosophers AND the entire body of modern scientists recognise the distinction between the orderliness of the cosmos, which allows us to infer natural laws, and the occasional destructiveness of events to mankind, which needs a different level of explanation.

Those who deny God  will take those phenomena as evidence of a malevolent or indifferent Universe. Classical theists will have various theodicies from God’s inscrutability to his judgements on sin. Only the Gnostics and other dualists would doubt that the universe was entirely subject to God’s ordering.

Kepler might well have pointed out that, given all those destructive forces, it’s instructive how few of Adam’s children have been killed by supernovae, colliding galaxies or asteroid strikes.


James R - #66534

December 13th 2011

beaglelady:

“But should scientists start investigations with a hard and fast conclusion of what they will find?”

No, they shouldn’t.  That is why they should not assume, for example, that a non-teleological explanation for the origin of life will eventually be available.  They should investigate the origin of life open to teleological as well as non-teleological explanations. 


beaglelady - #66542

December 13th 2011

Scientists have no way to investigate teleological claims, especially since no questions about the intelligent designer(s) are permitted.  But no matter, we’ll just let the next generation of Indian and Chinese students solve our scientific problems.


James R - #66544

December 13th 2011

beaglelady:

“Scientists have no way to investigate teleological claims.”

Scientists certainly do have ways of investigating teleological claims—the methods of design detection developed in a number of fields (archaeology, cryptography, forensic science, computer science, information theory, etc.) are recognized by all as scientific.

Isaac Newton, who knew a thing or two about science, certainly thought that design was detectable in nature, detectable enough that we could even infer things about God from it.  Read the General Scholium.  It may not be online, but there are bookstores and libraries where you can get it, if you want to know what a really good scientist thought.  (There are some, I realize who think that the members of the NCSE have a better understanding of the nature of science than Newton did, but I do not share that view.)

“But no matter, we’ll just let the next generation of Indian and Chinese students solve our scientific problems.”

This is what is called in logic a non sequitur.  It has no argumentative connection with the previous sentence.  Thus, its meaning in this context is obscure.


beaglelady - #66546

December 13th 2011

Scientists certainly do have ways of investigating teleological
claims—the methods of design detection developed in a number of fields
(archaeology, cryptography, forensic science, computer science,
information theory, etc.) are recognized by all as scientific.


I certainly wasn’t talking about archaeology, etc. where we are familiar with the identity, motivation, etc of the designers.

Isaac Newton, who knew a thing or two about science, certainly thought
that design was detectable in nature, detectable enough that we could
even infer things about God from it.


Isaac Newton certainly did invoke intelligent design…when he couldn’t figure out how the planets could maintain a stable orbit. He thought that God had to prod them occasionally in Intelligent Orbit Maintenance.     But Pierre-Simon de La Place came along and figured it out.   Now what if La Place had considered the problem unsolvable?  Do we want American school kids thinking that tough problems are unsolvable?






James R - #66549

December 13th 2011

beaglelady:

“I certainly wasn’t talking about archaeology, etc. where we are familiar with the identity, motivation, etc of the designers.”

What you said was that “scientists” (without restriction) “have no way to investigate teleological claims.”  Now you are admitting that some scientists can investigate such claims.  So your initial statement was incorrect.  You therefore need to restate, and then show the relevance of your point, whatever it is.

You do not appear to have studied Newton’s thought, but to be relying upon bits and pieces of stray knowledge picked up from popular sources.  (And apparently popular sources that spell “Laplace” in a non-standard way.)  I directed you to his General Scholium, but apparently you would rather argue about him based on hearsay rather than take the time to read what he wrote. 

Newton’s suggestion of adjustments to the planetary system to keep it stable has nothing to do with the design that I was talking about.  Your remark shows that you have confused “design” with “intervention.”  Until you get those two concepts distinguished, you are not going to understand the subjects we are talking about.

Nobody is advocating that American school kids should regard tough problems as insoluble.  But if you want to talk about science-stoppers—which is apparently your intention here—you might start by considering how inhibiting to science was the Darwinian inference that most of the DNA in the “noncoding regions” was useless junk left over from the vagaries of mutation over countless generations.  Starting from such an inference, one would never bother to look for unexpected functions.  Yet almost weekly now we discover new uses for noncoding DNA, just as design theory predicts.  So if we imagine two science teachers in a school, one saying, “Most of this DNA is almost certainly rubble left over from the evolutionary process, so don’t bother thinking about it,” and another saying, “It is quite possible that much or even most of the noncoding DNA has unknown but important functions, so we should study it carefully,” which one would you rather have teaching science to your children?


beaglelady - #66560

December 14th 2011

What you said was that “scientists” (without restriction) “have no way
to investigate teleological claims.”  Now you are admitting that some
scientists can investigate such claims.  So your initial statement was
incorrect.  You therefore need to restate, and then show the relevance
of your point, whatever it is.


Okay then, scientists can examine teleological claims about things made by humans.   We are familiar with what humans can do and have made in the past.  

You do not appear to have studied Newton’s thought, but to be relying
upon bits and pieces of stray knowledge picked up from popular sources. 
(And apparently popular sources that spell “Laplace” in a non-standard
way.)  I directed you to his General Scholium, but apparently you would
rather argue about him based on hearsay rather than take the time to
read what he wrote.


Such condescension!  There is no need for me to run out and read a book in this case. We both know that Newton invoked God to explain planetary motion.  Do you really think he didn’t?

Newton’s suggestion of adjustments to the planetary system to keep it
stable has nothing to do with the design that I was talking about.  Your
remark shows that you have confused “design” with “intervention.” 
Until you get those two concepts distinguished, you are not going to
understand the subjects we are talking about.

But both cases are extremely similar—invoke a deity when faced with scientific ignorance.   When did the design event(s) take place, when was the design handed off to be actualized, and how was this done?

Nobody is advocating that American school kids should regard tough
problems as insoluble.  But if you want to talk about
science-stoppers—which is apparently your intention here—you might start
by considering how inhibiting to science was the Darwinian inference
that most of the DNA in the “noncoding regions” was useless junk left
over from the vagaries of mutation over countless generations.  Starting
from such an inference, one would never bother to look for unexpected
functions.  Yet almost weekly now we discover new uses for noncoding
DNA, just as design theory predicts.  So if we imagine two science
teachers in a school, one saying, “Most of this DNA is almost certainly
rubble left over from the evolutionary process, so don’t bother thinking
about it,” and another saying, “It is quite possible that much or even
most of the noncoding DNA has unknown but important functions, so we
should study it carefully,” which one would you rather have teaching
science to your children?


Why the either/or? Why not teach the best up-to-date science?  Scientists know that non-coding DNA can acquire new function.  And BioLogos has, I believe, promised a post on so-called “junk DNA.”




 



James R - #66563

December 14th 2011

beaglelady:

You admit that design inferences are legitimate when we are dealing with things known to be artifacts.  Now, we cannot say at the moment whether the first cell arose accidentally, or was an artifact.  If the first cell was an artifact, design inferences (based on the analysis of copies and derivatives of that cell), would be entirely appropriate.  And precisely because we do not know which is the case, we have to keep the design option open. 

I never denied that Newton invoked God in order to explain why the solar system had not fallen into disarray after millions of years.  I did not ask you to confirm that claim from a book.  My point was that your objection to Newton was an objection to divine intervention, i.e., to breaking into nature in order to repair it.  But you cannot move logically from banning divine intervention to banning intelligent design, as is clear from the example of Newton.  If Newton could have been persuaded that the solar system had long-term stability, so that no future intervention would be necessary to keep it running, he would still have affirmed the solar system’s divine design.  It was that point on which I said you should read the General Scholium, since clearly you did not know that Newton accepted teleological reasoning.

Certainly we should teach the best, up-to-date science, but what happens when the “best, up-to-date science” is riddled with prejudice and unwarranted assumptions?  Ten or fifteen years ago, the “best, up-to-date science” would have taught school children the dogma of junk DNA, which was wrong.  But there was available during that period a scientific alternative, which expected to find function in much or most DNA, because it seemed a very reasonable inference that the whole DNA-protein system was designed.  You have not grasped:  neo-Darwinism made a falsified prediction about junk DNA, whereas design theorists made a confirmed prediction about it.  As for a possible upcoming Biologos column on junk DNA, you don’t have to wait for that:  Jonathan Wells’s new book on junk DNA is now out.  He’s spent about ten years studying the specialist, peer-reviewed literature on the subject.  (There are over 560 technical references in the notes.)  If you want to learn about the history and pitfalls of the junk DNA view, I would suggest his book as a good place to start.  


Terrance - #66569

December 15th 2011


Terrance - #66570

December 15th 2011


beaglelady - #66585

December 15th 2011

You admit that design inferences are legitimate when we are dealing with
things known to be artifacts.  Now, we cannot say at the moment whether
the first cell
arose accidentally, or was an artifact.  If the first
cell was an artifact, design inferences (based on the analysis
of copies and derivatives of that cell), would be entirely appropriate. 
And precisely because we do not know which is the case, we have to keep
the design option open. 



But you couldn’t tell freshly designed cells (made yesterday) from copies made from a designed first cell, could you?  I mean, when you talk about copies you are assuming a lot.  How would you know that copies are all we have now?  How would you know the designer has gone out of business?

 My point was that
your objection to Newton was an objection to divine intervention, i.e.,
to breaking into nature in order to repair it.  But you cannot move
logically from banning divine intervention to banning intelligent
design, as is clear from the example of Newton.  If Newton could have
been persuaded that the solar system had long-term stability, so that no
future intervention would be necessary to keep it running, he would still have affirmed the solar system’s divine design.  It was that
point on which I said you should read the General Scholium, since
clearly you did not know that Newton accepted teleological reasoning.



Certainly he did.  He also went overboard on his religious musings. 


Certainly we should teach the best, up-to-date science, but what happens
when the “best, up-to-date science” is riddled with prejudice and
unwarranted assumptions?



In other words, when it doesn’t agree with ID?






James R - #66587

December 15th 2011

beaglelady:

Your point about cells and copies of cells is expressed so obscurely that I have no idea what it means.  If I may make a suggestion regarding your writing:  it would help if you would employ normal expository prose— where each sentence is linked to the one before with the judicious use of conjunctions indicating logical relationship— instead of a series of apparently rhetorical questions, which seems to be your usual style.

The point about cells is that unless you are sure they are not artifacts, you cannot rule out the appropriateness of design language and the possibility of a designed (as opposed to accidental) origin for the first cell.  But as far as I can tell, you think that these two possibilities should be ruled out. 

I’m sorry that you disagree with Newton’s conception of science, and prefer that of Jerry Coyne and his friends.  I prefer Newton’s.

I’m sorry we also disagree about science education.  You apparently want it to be propaganda for whatever are the currently ruling views in the various sciences.  I would like it to be something quite different.  I think science education should put much more emphasis on how scientists come to their conclusions than on persuading students that the currently received conclusions are the right ones.  The idea of education is to train the students’ critical faculties, so that they can eventually discover things for themselves, not to encourage them to check out their critical faculties at the classroom door and passively accept expert or consensus views. 


beaglelady - #66589

December 15th 2011

James,

Just answer the questions and stop the insults.

Could you distinguish between a cell designed yesterday from a cell copied from the first cell?  Why or why not?

I’m sorry we also disagree about science education.  You apparently want
it to be propaganda for whatever are the currently ruling views in the
various sciences.  I would like it to be something quite different.  I
think science education should put much more emphasis on how scientists
come to their conclusions than on persuading students that the currently
received conclusions are the right ones.  The idea of education is
to train the students’ critical faculties, so that they can eventually
discover things for themselves, not to encourage them to check out their
critical faculties at the classroom door and passively accept expert or
consensus views.

Blah blah (ID)



Did you use to post here at BioLogos under the name of Rich?


beaglelady - #66590

December 15th 2011

Let me reword that, as I’m eating dinner and am distracted.

Could you distinguish a cell designed yesterday from a copy of the first cell?


James R - #66591

December 15th 2011

beaglelady:

I did not insult you.  I told you that I could not follow your reply, and I told you why, and I gave you a suggestion for altering your style so that you would be able to get your points across better to me and others.  If you took my constructive criticism as an insult, you misunderstood me.  I am striving for a polite style of exchange here.

But if we are going to speak of insulting people, you might ask yourself whether answering someone with “Blah, blah” could constitute an insult to someone who is making his best effort to make himself clear.

You write:  “Just answer the questions.”  I don’t respond to brusque demands that I answer questions, especially when the relevance and purpose of the questions are not clear to me.  If you have a point to make about the similarity or difference between an original cell and copied cells, just set forth your view, and explain to me how it is relevant to the point at issue, i.e., whether or not the first cell was an artifact.  After you have clearly set forth your view, I will respond.

I remember seeing a few posts by Rich.  I gather that he could sometimes be chippy in his remarks.  As you can see, I strive to be polite rather than chippy.  And if there are similarities between my ideas and those of someone else, I cannot help that.    
 


beaglelady - #66627

December 16th 2011

Could you distinguish a cell designed yesterday from a copy of the first cell?  You could answer the question. 

Also, did you at one time post here at BioLogos under the name of Rich? A yes or no answer would be appropriate.


James R - #66630

December 16th 2011

beaglelady:

Regarding your second question, I was under the impression that I had already answered it.

Regarding your first question, I have no idea what it is driving at.  I asked you how you personally determined that the first cell was not an artifact.  When you give me a full account of why you believe that the first cell was not an artifact—what your evidence is that it couldn’t have been an artifact, or probably wasn’t an artifact, and what your alternative explanation for the first cell is—and I want real exposition here, two or three paragraphs of your own thought, not quotations of others, not references to TV specials or museum lectures, but your own coherent exposition, and all in indicative rather than interrogative sentences—then, I promise, I will try to answer your question.  (Hopefully your explanation of your view will give me enough insight into your reasoning that I can figure out what on earth your question is driving at.)


beaglelady - #66637

December 16th 2011

No, you didn’t answer my second question at all. It was a simple question and I would expect a yes or a no. That’s not a lot to ask, is it?

Regarding your first question, I have no idea what it is driving at.  I
asked you how you personally determined that the first cell was not an
artifact.  


Why should I have to personally determine that the first cell was not an artifact? Have you personally determined that other cells are not artifacts?  How would one do that?  And how does one control for designer(s) in scientific experiments today, or has he/it been inactivated?
 

btw why is it not okay to refer to museum lectures by scientists when you refer me to someone like Jonathan Wells?   If he has something to say about so-called “junk dna” why doesn’t he publish his research in peer-reviewed journals for scientists to evaluate?



James R - #66639

December 16th 2011

“No, you didn’t answer my second question at all. It was a simple question and I would expect a yes or a no. That’s not a lot to ask, is it?”

No.


beaglelady - #66645

December 17th 2011

Okay, it’s not a lot to ask.

So tell us! Did you at one time post here at BioLogos under the name of Rich?


James R - #66649

December 17th 2011

beaglelady:

I suggest that, at your next annual physical exam, you have your hearing tested.  You’ve been answered twice.

Speaking of not answering questions, you have repeatedly refused to state your position on whether or not the first cell was designed and to explain how you arrived at your conclusions.  I can only infer that you do not discuss the issues that I wish to discuss, and therefore, that there is no point in our continuing this conversation.  I therefore take my leave of this thread. 


beaglelady - #66652

December 17th 2011

You still haven’t answered yes or no, James.
Why is that?

And no, I don’t believe that the first cell was designed.  I don’t think there was any need for a first cell to be designed. I think God’s natural world is quite capable of bringing forth life without extra prodding or pushing.  But certainly there is no way to tell for sure.  Similarly, there is no way to tell if a designer is designing new cells at this very moment.  (It could be high time for an upgrade.) But we have no way of telling for sure, do we?

btw, when did this supposed design event occur? And how was the design actualized?


HornSpiel - #66651

December 17th 2011

James,

Forgive me for jumping in here. but I see below that you state that you have ended your dialog with beaglelady (on this thread). But I have a few thoughts on the first cell question.

Firstly, however, your question has an element of semantics in it: What do we mean by design and artifact? So let me define my terms.

I consider something to be designed if it is created by a contingent intelligence, i.e. a creature. In the same vein, I only consider artifacts to be made by contingent intelligences, not by the ultimate uncreated creator (unless you take the universe, as a whole, as an artifact.)

I believe God created the world and the whole pattern of  creation is suffused with design, but that design is a result of the"natural laws” that science describes, plus providence. Natural laws are God’s normal way of sustaining the universe (Col 1:16).  Providence is Gods ability to work though circumstance to bring about His ends  (Rom 8:28).  Providence allows the “improbable” to be realized within the framework of natural law.

Therefore, the first cell was created not designed (Gen 1:1 ) I am using biblical language purposefully. Likewise I do not separate design and manufacture because the Bible says God makes things. The psalmist says: “I am fearfully and wonderfully made,” and  “You knit me together in my mother’s womb.”  This can only be true if natural biological processes are God at work.

So I believe the first cell was realized though a combination of natural laws and specific circumstances, which may or may not have had a likely probability of occurring on the primordial, abiotic earth. It was a natural miracle, an amazing and wonderful act of creation. I reject the notion that life is an artifact of any previously existing super-intelligent being, as there is no evidence for this and/or it implies a demiurge type of universe. Likewise I reject ID as it opens up science to this kind of speculation.

The kind of “design” ID claims to be able to detect, is to me “miraculous intervention detection” which I do not believe is possible. Biblically God’s interventions in history are called signs, and are one-off events intended to make a specific point. Creation is not miraculous in that sense. It points to God, but not though “design hotspots.”

I know you will disagree, and I am not really interested in furthering the discussion of this subject on this page (we can perhaps pursue it elsewhere). I am just trying to present a view that I hope addresses your question.


James R - #66653

December 17th 2011

Hornspiel:

I’ll make you a deal.  I’ll reply to this post of yours, and you in turn will go back to the previous page and reply with some degree of engagement to my long reply 66533, which you previously quickly dismissed.  Fair?

First, let me say that I’m familiar with the Biblical terminology, and also with the uses of terms like “artifact”, “nature” etc. in philosophy, theology, and the history of ideas.  This (including the Hebrew text of Genesis 1-11) is all material I’ve taught at the university level.  Having said that, let me grant your point right away, that “artifact” is an ambiguous term and that my meaning might not have come across the way I wanted it to.

Yes, you are right to point out that in its original usage, “artifact” refers to man-made objects—things made by human art.  By extension it could be applied to beaver dams or beehives, if you regard the activity of those animals as “art” in some sense.  I was extending the term to denote the result of the creative action of God.

I grant you that any application of the term to God would be using analogy.  And I would be the first to say that God does not design or make things literally as human beings make things.  All analogical language regarding God must be filled with qualifications.

Nonetheless, the Christian tradition is clear that God is “maker of heaven and earth”.  And in various places the Bible uses anthropomorphic language to describe God’s making (Genesis 2: “forming” out of the dust of the ground, references to plumb lines in Job, etc.)  Genesis also indicates also that God plans before he acts (and yes, I’m aware of the difficulties of “before” in reference to God, but that is the Biblical language) — see Genesis 1, where each thing is projected before it is made.  So the language of design and artifact is not entirely un-Biblical.

However, if you want to restrict terms like “artifact” and “design” to the products and actions of contingent intelligences, you can; but then, since both the Bible and the tradition are very clear that God something-like-designed and something-like-made the world, we need some other word to denote what is analogous to “designing” and “making” in the case of God.  I am open to suggestions.  

“Created not designed” is not a good formulation of the Biblical teaching.  Creation clearly involves God’s projection beforehand of something (Genesis 1); God has the “design”—the look, structure, and mechanical organization—of each thing in mind.  You would be more accurate to say that creation means something more than design, or is deeper than design. 

To put it simply, all I meant by “artifact” in this context was something “produced by intelligence” rather than “produced solely by the blind action of chance and natural laws”.  The cell was in fact first produced by God’s intelligence, and that is what I mean by calling it an artifact.  If you refuse the term “artifact”, that is fine; but if you know what I mean, and agree with me, then I could accept another term.

The actual process by which the design was implemented may have involved wholly natural causes, wholly supernatural causes, or a combination.  That question is immaterial to the point I am making.  The point is that—in my view—there wouldn’t be any cells in the universe if someone had not “designed” them.  Substitute any word you wish for “design.”  I am saying that nonintelligent causes alone would not be enough.  That is why they are “artifacts.”

It is a failure to distinguish between design/chance and supernatural/natural that has confused beaglelady.  She thinks I am asserting that the first cell was assembled miraculously.  It may well have been.  But it need not have been, in order for that first cell to have been designed.  And if it was designed, then it is an artifact in the sense that I am using the word.   

(Continued in next post)


HornSpiel - #66655

December 17th 2011

Respectfully James, I am going to pass on your offer. My point was not  to engage you in a debate but to respond to your question in a way that contrasted what I believe, with what I regard as the inevitable logical and theological implications of the ID position.



James R - #66656

December 18th 2011

HornSpiel:

If you don’t want to discuss any of my three posts (two here and one on the previous page), I have to accept your decision.  I am sorry that the material in them is not tantalizing enough to induce you to further discussion, queries, and debate.  But I hope you will re-read them in a leisurely moment and think about them.  They are the result of thirty-odd years of teaching and scholarship on the subjects of “creation” and “nature,” and I offered them with your interest at heart, since you seem to be genuinely thoughtful about these matters. 

Regarding your last clause, the difficulty is that you do not understand “the ID position” correctly, and therefore your deduction of “the inevitable logical and theological implications” of that position is faulty.  You started, in your comment to Jon Garvey which I referred, to grasp ID more accurately; but now you have pulled back from that, and settled into the erroneous understanding of ID that has been propagated by Collins, Giberson, and other TEs, as well as some of the atheistic writers.  If you wish to base your inferences on an incomplete and misleading understanding of ID’s claims, I cannot stop you.  But I would naturally prefer that you took the more cautious approach and familiarized yourself to a much greater level with ID writings before drawing the conclusions that you have drawn.

Perhaps we shall meet again on another thread.


James R - #66654

December 17th 2011

Hornspiel (Part 2 of 2):

You have said that “the whole pattern of creation is suffused with design.”  I agree.  And so, by the way, does every ID proponent known to me.  (On the other hand, TEs Ken Miller and Francisco Ayala do not agree that everything is suffused with design; they have said specifically that natural evils are not designed by God, but arise due to blind Darwinian processes.)

When you say that the origin of life was “a natural miracle,” you may be correct, but you cannot verify it, because you were not there.  Nor can “science” teach you that.  Science at the moment is not even close to explaining how life could arise from non-life, and it may never be able to do so.  If you think you know that the first cell arose from wholly natural causes, without any supernatural intervention, your knowledge comes not from science but from a theological assumption about the way that God would have done things.  You cannot claim the authority of “science” for that assumption.

I have already told you that your view of ID—that it requires miraculous intervention—is incorrect.  And if you noticed, I praised your reply to Jon Garvey when you showed the first signs of emerging from that error and realizing that ID was not inherently tied to miraculous interventions.  But now you have slid back into your old way of thinking.

I am fully aware of the various Greek and Hebrew terms used for “sign”, “miracle” etc.  I am also fully cognizant of the argument you are making here to restrict the use of the term “miracle”—it has been argued by TEs for over 20 years now, and I would be a wealthy man if I had $100 for every time I had heard it.  What the argument overlooks, among many other things, is that in the Bible the “mighty acts of God”, such as the liberation of Israel, acts which are clearly miraculous in terms of the vocabulary of “signs” etc., are frequently likened, either by direct reference or by literary allusion, to aspects of the account of Creation.  It is merely pedantic make a big deal out of the fact that the word “miracle” is not used in Genesis, if the general Biblical context indicates that the Biblical authors saw the days of creation as setting forth the first of God’s “mighty acts.”

I am not arguing that God could not have used a natural process to bring about the cosmos, life, and man.  I am willing to view the Biblical language in a less than literal way, and to free up thought about origins from the detailed words of Genesis 1.  But you were the one who raised the “Biblical view” here, so I am responding with some considerations about how the Biblical authors appear to have thought about these matters.  Even if we take Genesis 1 non-literally regarding the actual sequence of events, there is no doubt that God’s planning was intended.  In that sense, cells, plants, animals and human beings were all designed, and are “artifacts” in a readily comprehensible sense of the word, when the contrast with “chance and necessity” is kept in mind.


Terrance - #66571

December 15th 2011


Terrance - #66572

December 15th 2011

James R

You accuse commenters here of not reading ID literature, but it would seem that you have read very little actual scientific literature. Most of your knowledge of biology appears to have been acquired from Uncommon Descent. If you had read original research articles, you would know that the whole ID/creationist “Darwinists said all of this DNA was just junk and now we have found it has all these functions” trope is completely and utterly bogus. It is not merely slightly misleading, or based on a minor misunderstanding, it is a deliberate misrepresentation of the entire field of molecular biology.

First of all, there has always been a diversity of views among biologists as to what percentage of the genome is ‘functional’ (ironically strict Darwinian adaptationism predicts a large degree of functionality in the genome - so “Darwinians” did not “preach junk DNA”). In his original paper in which he coined the term ‘junk DNA’ (admittedly a pretty lamentable choice) Ohno even listed potential functions. Furthermore, it was not simply an argument from ignorance; assuming it to be useless in the absence of any understanding of it. There are various scientific reasons for believing that much of the genome does not have a function. It is even more ridiculous to claim it was a “science-stopper” or that ID was a “science-promoter” in this instance. Who did all of the research that unearthed all of these ‘functions’ that ID advocates cite? It certainly wasn’t the ID advocates themselves. And why would scientists have been wasting their time investigating DNA they thought did nothing? The whole tale doesn’t even have basic plausibility, never mind sufficient verisimilitude to fool anyone with access to Google or the ability to read scientific articles and glean a basic understanding of the main points.


James R - #66575

December 15th 2011

Terrance:

I’ve noticed that on a couple of threads here, you seem to have technical problems posting.  Your name appears above, three times, with nothing under it, and this has happened before.  Perhaps you should contact the technical team and get some help using the software.

I haven’t learned much biology from Uncommon Descent; in fact, I read very few posts at that site.  You are more likely to find me reading the original works of Charles Darwin, George Gaylord Simpson, Jacques Monod, Stephen Jay Gould, etc.

When you speak of “a deliberate misrepresentation of the entire field of molecular biology” you are engaging in rhetorical exaggeration.  A criticism of one particular view regarding one aspect of the genome (the noncoding DNA) distorts the entire field of molecular biology—a field which studies much more than DNA?  If you want a serious intellectual discussion, please avoid such over-the-top rhetoric. 

You make an interesting point about strict adaptationists.  I can see that for them, junk DNA would be expected to be minimal.  However, Darwinian theory is a big tent, and not all Darwinians are strict adaptationists, as you ought to know, given the expertise you are intimating.  

In answer to your question “Who did all the research that unearthed all of the functions?”, the answer is easy:  scientists who were not blinkered by the view that most of the non-coding DNA is probably useless; scientists who had a truly empirical orientation, and followed the evidence wherever it led.  I have nothing but praise for such scientists.  That is what biology needs: more empiricism, less doctrinaire theorizing about origins.

I don’t claim any expertise on the technical literature on junk DNA.  Jonathan Wells, however, does keep up with the technical specialist literature on evolutionary theory, developmental biology, and other fields, and having made a special study of  junk DNA, he is quite conversant with the entire history of the debate.  That’s why I recommended his book to beaglelady, who, based on her comments, appears not to be a scientist and therefore would find a guide to the junk DNA debate useful.

I assume from the tone of your objections that you see yourself as a representative of good biological science.  Whether this means you are claiming a Ph.D. and research accomplishments in some field of biology, I do not know.  But if you have such expertise, it should be child’s play for you to read Wells’s new book, and check out a sampling of 30 or 40 of his 500+ citations of technical literature in the original journals to see if he has fairly represented the contents of the articles.  Perhaps then you can come back here and explain to us what it is that he has misunderstood about the debate.  That would be a more scholarly procedure than citing the very partisan Steve Matheson as an objective judge of Wells’s work.


beaglelady - #66586

December 15th 2011

That’s why I recommended his book to beaglelady, who, based on her
comments, appears not to be a scientist and therefore would find a guide
to the junk DNA debate useful.


You aren’t a scientist either. At least I get out and hear scientists give lectures.

btw, did you use to post here at BioLogos under the name of ‘Rich’ ?


Terrance - #66573

December 15th 2011

...
Instead of learning genetics from Casey Luskin and molecular biology from Jonathan Wells I’d suggest you acquaint yourself with the original research. As an introduction you might want to look through Steve Matheson’s –  http://sfmatheson.blogspot.com/  - articles entitled “Talking trash about “junk DNA.””


beaglelady - #66588

December 15th 2011

Terrance,

Your link doesn’t work (isn’t this editor a piece of garbage?)

I believe this is what you were linking to:

http://sfmatheson.blogspot.com/2007/12/talking-trash-about-junk-dna.html


Chip - #66584

December 15th 2011

I’m late to the party, but just wanted to say thanks to Jon and James, whose contributions have made this one of the most interesting exchanges I’ve ever read on BL. 


James R - #66607

December 15th 2011

Nice of you to say so, Chip.  I’m glad if I’ve been of any use.


PNG - #66609

December 16th 2011

I really don’t understand this obsession with finding all the genome to be functional. Even if one conceded the ID point of view, that design can be scientifically proven (which I don’t accept), it doesn’t follow that all or even most of the genome has to be functional. It’s apparent that mammalian genomes grew by the insertion of millions of transposable elements (TEs) and other repetitive sequences over a long period of time (the same is true for many plants and other organisms), and the process is still going on. A very recent paper using methods more sensitive than the usual Repeat Masker software found that as much as 2/3 of the human genome may have started as transposable element copies. The sequencing of a few hundred individual human genomes has resulted in identifying thousands of recent TE insertions (7400 in a recent accounting) that are not fixed in the population, and there is every reason to expect that in the whole human population there are hundreds of millions of new insertions at any time. It should be obvious that sequences that were recently inserted and are present in only some people can’t have any necessary function in the genome. Also, the fact that sequences that are anywhere from 100-6000 bp long can be dropped into the genome at more of less random positions and rise to high allele frequencies is in itself pretty good evidence that most of the genome has no function. 


At the moment if you add up all the conserved sequences and other sequences for which there is some evidence of function and then make a large allowance for future discoveries of function (double all the known functional sequence) you get maybe 15% of the genome being functional, which is similar to other recent estimates based on other assumptions.

You may regard Steve Matheson as a partisan because he disagrees with you, but in fact he is a very well read and accomplished researcher and anyone who is unfamiliar with this particular tempest in a teapot would do well to read his posts. Larry Moran also wrote an extensive review of Well’s book, and, although I don’t agree with Moran’s atheism and I often don’t like his manners, he is a knowledgeable biochemist and I think it is fair to say he demolishes the book effectively.

The fact is that whatever may have been hypothesized about the gene deserts of mammalian genomes, molecular biologists have continued to work on them and there never was any “science stoppage” as a result of these hypotheses. The so-called “myth of junk DNA” looks to me like an attempt by people who haven’t done any actual research to get some of the credit that belongs to the people who did the research that told us what us we know about repetitive DNA.

If you want to know about me, I am a biochemist (Ph.D.) and I did research for about 30 years. I have followed the TE literature since about 1990 when I realized that it was overwhelming evidence for common descent. I also had a department colleague whose lab studied mouse L1 elements, so I had an expert to address questions to. Maybe it’s also relevant (this only occurs to me now) that I spent a lot of time (too much, in retrospect) looking for a function for a universal class of metabolites. There were a bunch of us all over the world who thought that a particular class of dinucleotides really looked like they should have an important function in cells, but no one could ever find a function. We found the enzymes that synthesize and degrade these things, and one of those turned out to be a tumor suppressor, but this apparently had nothing to do the metabolites. As far as anyone could tell it was just metabolic junk that formed because chemically activated nucleotides that are bound to enzymes can react with other nucleotides readily. Metabolic junk happens, and cells have enzymes to get rid of it. It’s possible that someone will find a function for these things in the future, but right now it looks like junk.

I can understand why people who aren’t biochemists can look at living things and say “they are so amazing that they must be brilliantly designed,” but if you are a biochemist you know that cells make a lot of mistakes. Errors happen in DNA, RNA and protein synthesis. Nonfunctional small molecules get made. Devastating mutations happen. The immune system overreacts and kills the animal instead of curing it. In light of this kind of thing, it’s not surprising to find that there is a lot of DNA sequence that doesn’t do anything. The fact that living things are amazing doesn’t mean that they are perfect. They aren’t. It seems to me that the expectation that all the genome should be functional is just a naive expectation that isn’t supported by the evidence and it isn’t even implied by a design perspective, unless by “design” one means perfect, 100% efficient design.

 


James R - #66610

December 16th 2011

PNG:

Design theory doesn’t require that all of the genome should be functional.  It’s compatible with the accretion of non-functional elements.  But it would predict that most of the genome, including most of the “noncoding” portion, will have function.

When you speak of things that “people who aren’t biochemists” wouldn’t know, don’t forget that Michael Behe is a biochemist.  He is quite aware of all the facts you point out, and of all the apparently non-designed aspects of living systems.  This has not prevented him from seeing an overall design.  As for the errors in copying, protein synthesis, etc., yes, they are there, but they are remarkably few, fewer than the errors in most if not all human-designed systems.  Remember that “designed” does not mean “flawless”.  The Edsel had flaws, but it was still designed, not the product of chance.

Your 15% functionality estimate is an argument from ignorance.  I don’t mean that you personally are ignorant in a pejorative sense.  I mean that, if it is an argument from ignorance to say:  “We don’t know any natural mechanism that could do this, so therefore God must have done it miraculously”, it is equally an argument from ignorance to say:  “We can’t see any functionality for this DNA at the moment, so we won’t find any in the future, and at best, we will only find functionality for 15% of it.”  No one is in a position to say that.  Especially not a Christian, who must believe that God’s intellect is far beyond human intellect and that his wisdom is subtler than we could ever imagine.  We may have only scratched the surface in our understanding of the genome.  

Your remark, “You may regard Steve Matheson as a partisan because he disagrees with you” imputes a low motive to me, and is unjust.  My remark was based not on his position but on his debating style, as exemplified in his blogs and other internet appearances (with the exception of his recent columns here, which are more moderate and balanced in their dialogical approach).  In any case, Wells has written an entire book on junk DNA, with nearly 600 references to state-of-the-art peer- reviewed literature.  Matheson’s field of expertise is developmental biology, not junk DNA.  Why would you take Matheson’s word against that of Wells, in an area where Wells has done much more research than Matheson?  Could it be that you are doing what you accuse me of doing, i.e., choosing to agree with the person who takes your side of the debate?  As for Moran, he is a biochemist, not a geneticist, and evolutionary theory is his hobby, not his academic specialty.  He hasn’t a single peer-reviewed publication in the field.  And finally—correct me if I am wrong—it appears that you have decided that Wells is wrong without actually reading his book, basing yourself entirely on the reviews of his ideas by Moran and Matheson.  Is this what you as a Ph.D. in biochemistry regard as proper scientific procedure, to judge the value of a scientific book you have not read, based on what its critics say about it?


S. cerevisiae - #66615

December 16th 2011

James R, you have written (yours in italics):
Ten or fifteen years ago, the “best, up-to-date science” would have taught school children the dogma of junk DNA, which was wrong.

First the vast majority of eukaryotic DNA having no known function both then and now is an observation, not dogma, in what way was the observation wrong? Please note that YOU are claiming that something is wrong, so you can’t pass the buck to Wells.

But there was available during that period a scientific alternative, which expected to find function in much or most DNA, because it seemed a very reasonable inference that the whole DNA-protein system was designed.

So, James, please tell us quantitatively how much DNA was known to have function 10-15 years ago, and how much is known to have function today. After all, if you’re going to throw around accusations of using dogma, you ought know exactly what you are talking about. Numbers, please. Then and now. Very simple.

You have not grasped:  neo-Darwinism made a falsified prediction about junk DNA, whereas design theorists made a confirmed prediction about it. 

You don’t appear to have grasped that “isms” don’t make predictions, hypotheses do. Please state the mechanistic hypothesis without reference to people or isms, state the quantitative predictions, and explain quantitatively how it they have been falsified or confirmed. 

YOU are making these concrete claims, so please don’t point us to a book that says what you want to hear and has lots of citations. That would scream that you have very, very low motives.

S. cerevisiae - #66617

December 16th 2011

In any case, Wells has written an entire book on junk DNA, with nearly 600 references to state-of-the-art peer- reviewed literature.

Since you seem to be quantitative when it comes to references to the literature, how many of the <600 have you personally read? How many has Wells read? How many of the >>1000 authors of the state-of-the-art peer-reviewed papers would agree with Wells?

How many references does a competent 5-page review paper have? Contrasted with the citations/pages ratio of Wells’s book, is the book thin or thick with references? How many base pairs of the human genome could be explained a mere 600 references?

Matheson’s field of expertise is developmental biology, not junk DNA.  Why would you take Matheson’s word against that of Wells, in an area where Wells has done much more research than Matheson?

Wells has done zero research. 

Could it be that you are doing what you accuse me of doing, i.e., choosing to agree with the person who takes your side of the debate?

I don’t think so. Could it be that the fact that you’ve referred three times to the number of citations in Wells’s book and zero times to any of the data in the cited papers suggests that you have no real confidence in Wells’s conclusions?

As for Moran, he is a biochemist, not a geneticist, and evolutionary theory is his hobby, not his academic specialty.

Oh, my-you couldn’t be more wrong! 

On what basis do you make such an spectacularly false claim? Moran is BOTH an evolutionary biologist and a geneticist. Do you realize how foolish this makes you look in the eyes of those who know anything about Moran’s research?

Is Wells a geneticist? Is evolutionary theory Wells’s academic specialty?

He hasn’t a single peer-reviewed publication in the field.

Golly, you sound confident!

Proc Natl Acad Sci U S A. 1990 Feb;87(3):1159-63.
An essential member of the HSP70 gene family of Saccharomyces cerevisiae is homologous to immunoglobulin heavy chain binding protein.

That’s not genetics?

Does Wells have any genetics publications? Does Wells have a single first-author peer-reviewed publication in ANY field? Has Wells ever published a peer-reviewed publication as an independent scientist?

And finally—correct me if I am wrong—it appears that you have decided that Wells is wrong without actually reading his book, basing yourself entirely on the reviews of his ideas by Moran and Matheson.

I don’t see any evidence of that. In fact, PNG pointed out her/his understanding of L1 elements. What do YOU know about them? 

Is this what you as a Ph.D. in biochemistry regard as proper scientific procedure, to judge the value of a scientific book you have not read, based on what its critics say about it?

You have established neither that PNG hasn’t read it nor that PNG’s position was based on Moran’s review. You don’t even realize that Wells is not a geneticist, but Moran is! Doesn’t that claim blow your fallacious argument from authority right out of the water? I’ll bet that your conclusion has zero dependence on the argument you’re advancing here. Am I right? 

S. cerevisiae - #66618

December 16th 2011

Once more, with proper formatting (James R in italics):
In any case, Wells has written an entire book on junk DNA, with nearly 600 references to state-of-the-art peer- reviewed literature.

Since you seem to be quantitative when it comes to references to the literature, how many of the <600 have you personally read? How many has Wells read? How many of the >>1000 authors of the state-of-the-art peer-reviewed papers would agree with Wells?

How many references does a competent 5-page review paper have? Contrasted with the citations/pages ratio of Wells’s book, is the book thin or thick with references? How many base pairs of the human genome could be explained a mere 600 references?

Matheson’s field of expertise is developmental biology, not junk DNA.  Why would you take Matheson’s word against that of Wells, in an area where Wells has done much more research than Matheson?

Wells has done zero research. 

Could it be that you are doing what you accuse me of doing, i.e., choosing to agree with the person who takes your side of the debate?

I don’t think so. Could it be that the fact that you’ve referred three times to the number of citations in Wells’s book and zero times to any of the data in the cited papers suggests that you have no real confidence in Wells’s conclusions?

As for Moran, he is a biochemist, not a geneticist, and evolutionary theory is his hobby, not his academic specialty.

Oh, my—you couldn’t be more wrong! 

On what basis do you make such an spectacularly false claim? Moran is BOTH an evolutionary biologist and a geneticist. Do you realize how foolish this makes you look in the eyes of those who know anything about Moran’s research?

Is Wells a geneticist? Is evolutionary theory Wells’s academic specialty?

He hasn’t a single peer-reviewed publication in the field.

Golly, you sound confident!

Proc Natl Acad Sci U S A. 1990 Feb;87(3):1159-63.
An essential member of the HSP70 gene family of Saccharomyces cerevisiae is homologous to immunoglobulin heavy chain binding protein.

That’s not genetics?

Does Wells have any genetics publications? Does Wells have a single first-author peer-reviewed publication in ANY field? Has Wells ever published a peer-reviewed publication as an independent scientist?

And finally—correct me if I am wrong—it appears that you have decided that Wells is wrong without actually reading his book, basing yourself entirely on the reviews of his ideas by Moran and Matheson.

I don’t see any evidence of that. In fact, PNG pointed out her/his understanding of L1 elements. What do YOU know about them? 

Is this what you as a Ph.D. in biochemistry regard as proper scientific procedure, to judge the value of a scientific book you have not read, based on what its critics say about it?

You have established neither that PNG hasn’t read it nor that PNG’s position was based on Moran’s review. You don’t even realize that Wells is not a geneticist, but Moran is! Doesn’t that claim blow your fallacious argument from authority right out of the water? I’ll bet that your conclusion has zero dependence on the argument you’re advancing here. Am I right? 

James R - #66623

December 16th 2011

S. cerevisiae:

Your tone is inappropriate to collegial discussion.

Moran’s department is biochemistry, not biology (where genetics is normally studied), but I gladly concede that he knows something about genetics and that he has published articles in that field.  So I stand corrected:  let’s call him a geneticist.

What I was trying to say was that he has not published in journals that are specifically dedicated to evolutionary biology (as opposed to molecular biology, genetics, developmental biology, etc.).  He is not an “evolutionary biologist” in the sense that Jerry Coyne, Allen Orr and Sean Carroll are.  An evolutionary biologist publishes articles on evolutionary mechanisms and evolutionary pathways.  Moran writes about these things on his blog in a popular way, but I am unaware of any peer-reviewed articles of his dedicated to specific explanations of how A could have evolved into B or dedicated entirely to broader questions of mechanism in evolutionary theory.   I do not have access to the article you cite, but merely pointing out homologies in biomolecules does not constitute an evolutionary explanation.  However, if he has published peer-reviewed technical articles that are entirely dedicated to evolutionary pathways or discussions of evolutionary theory (as opposed to articles on genetics or biochemistry with an evolutionary gloss), point them out to me and I will retract my statement.  I have no desire to misrepresent Larry Moran’s qualifications or interests in order to score debating points.

Yes, Wells has published at least one solo peer-reviewed article in a recognized biology journal, and yes, he has been doing research for years now.  He held a poster session on his newest research at a major biology conference earlier this year.  You must have missed that conference.

If PNG tells me that he has read Wells’s book, I will take his word for it.  His wording suggested otherwise.
He also indicated that he was influenced by Moran’s review, and Matheson’s.  I did not attempt to misrepresent him.

I have found, in the past, that on Biologos, threads tend to wander from their original subject.  The subject here is scientific paradigms.  But you appear to be taking the discussion in a different direction, toward either defending the wounded amour propre of Darwinian biologists whose views a non-specialist has dared to criticize, or attacking the qualifications of ID proponents.  I’m not interested in such culture-war discussions.  If you have something interesting to say about the nature of scientific paradigms, I’m all ears.  But I won’t reply to any further hectoring of the sort displayed in this post.  Such “my side is smarter than your side” debating belongs on Panda’s Thumb, TalkOrigins, or Pharyngula.  I fear that you have caused me to slip into such a debating style myself, and I’m bringing that to an end right now.  Good day to you, sir.     


S. cerevisiae - #66625

December 16th 2011

Your tone is inappropriate to collegial discussion.

Really? What’s the tone of a false statement about qualifications? What’s the tone of a cocky, definitive statement that you refuse to support? Again, back to the meat of it:

Ten or fifteen years ago, the “best, up-to-date science” would have taught school children the dogma of junk DNA, which was wrong.

Do the decent Christian thing and support this claim with numbers and evidence or retract it. It’s black-and-white.

Moran’s department is biochemistry, not biology (where genetics is normally studied), but I gladly concede that he knows something about genetics and that he has published articles in that field.  So I stand corrected:  let’s call him a geneticist.

Please. You’re just digging deeper. If you believe what you’re claiming, perhaps you should complain to Stanford, where the Dept. of Biochemistry has two past presidents of the American Society for Cell Biology! Or maybe you should tell them that their Dept. of Genetics should be a part of Biology and not even exist! Do you realize how silly it was to stop with Moran’s department name? What does that suggest about the depth of your other scientific opinions?

What I was trying to say was that he has not published in journals that are specifically dedicated to evolutionary biology (as opposed to molecular biology, genetics, developmental biology, etc.).

Sorry, your revision is not credible. As a place for evolutionary genetics, PNAS is far better than any specialty journal. You clearly don’t understand the hierarchy of biology publications. You didn’t even read the abstract, man!

He is not an “evolutionary biologist” in the sense that Jerry Coyne, Allen Orr and Sean Carroll are.  An evolutionary biologist publishes articles on evolutionary mechanisms and evolutionary pathways.

You haven’t bothered to READ any of Moran’s papers, so how can you be credible on this count, James? He’s a geneticist. Regardless of ANY evolutionary implications, he knows much more about the functional/junk ratio than you or Wells ever will.

What’s that ratio today and how much has it changed in the last 10-15 years, BTW?

Moran writes about these things on his blog in a popular way, but I am unaware of any peer-reviewed articles of his dedicated to specific explanations of how A could have evolved into B or dedicated entirely to broader questions of mechanism in evolutionary theory.

So what? You definitively claimed that he wasn’t a geneticist and therefore wasn’t as authoritative as Wells, when in fact the opposite is true. You’re just demonstrating that you’re not aware of the things you write about and that you didn’t derive your conclusion from your premises. Is Wells a geneticist? Is evolutionary theory Wells’s academic specialty?

…point them out to me and I will retract my statement.

You haven’t retracted any of your other objectively false statements yet!

S. cerevisiae - #66626

December 16th 2011

Yes, Wells has published at least one solo peer-reviewed article in a recognized biology journal, and yes, he has been doing research for years now.

Then cite it! Why are you changing the criteria?

He held a poster session on his newest research at a major biology conference earlier this year.  You must have missed that conference.

I’m sorry, but you aren’t making any sense at all. Conferences hold poster sessions and people present posters at them. Presenting a poster is NEVER referred to as “holding a poster session.” Besides, posters aren’t peer-reviewed, and I suspect that you know that. Which meeting?

If PNG tells me that he has read Wells’s book, I will take his word for it.  His wording suggested otherwise.

Golly. Your wording doesn’t merely suggest, it STATES that there is some “junk DNA dogma” that is simply wrong, but you neither clarify nor support that.

He also indicated that he was influenced by Moran’s review, and Matheson’s.  I did not attempt to misrepresent him.

He wrote nothing whatsoever about being influenced by them, he simply recommended them. It’s pretty clear that PNG knows her/his stuff and you don’t. That was indeed a gross misrepresentation. Was it intentional? 

I have found, in the past, that on Biologos, threads tend to wander from their original subject.  The subject here is scientific paradigms.

Back to them, then! You wrote,

Ten or fifteen years ago, the “best, up-to-date science” would have taught school children the dogma of junk DNA, which was wrong.

I’ve asked you to clarify and support that, and you have done neither while whining about my tone.

Where does Wells offer a number, James? What page? That’s dead on the subject of scientific paradigms and a concrete claim that YOU made about a scientific paradigm.

But you appear to be taking the discussion in a different direction, toward either defending the wounded amour propre of Darwinian biologists whose views a non-specialist has dared to criticize, or attacking the qualifications of ID proponents.

YOU offered an utterly false contrast between Wells and Moran, remember? Do you think that a little French effectively conceals that?

If you have something interesting to say about the nature of scientific paradigms, I’m all ears.  

I do and you’re not.

Such “my side is smarter than your side” debating belongs on Panda’s Thumb, TalkOrigins, or Pharyngula.

What would anyone call the following false claim, pot? 

“As for Moran, he is a biochemist, not a geneticist, and evolutionary theory is his hobby, not his academic specialty.  He hasn’t a single peer-reviewed publication in the field.”

I fear that you have caused me to slip into such a debating style myself, and I’m bringing that to an end right now. 

Please. You were in that style days ago!

You have not grasped:  neo-Darwinism made a falsified prediction about junk DNA, whereas design theorists made a confirmed prediction about it.

Argon - #66669

December 18th 2011

James R: “As for Moran, he is a biochemist, not a geneticist, and evolutionary theory is his hobby, not his academic specialty.

Dude! Laurence (Larry) Moran’s division in the Biochem department at the University of Toronto is Proteomics and Bioinformatics, His area of research is listed as “Molecular Evolution”. He maintains the HSP70 sequence database a collection of data & phylogenies from organisms across all domains/kingdoms of life. He knows his sh*t when it comes to biochemistry and molecular biology having taught the subject an written a solid college-level textbook in the area (now in its fifth edition). Well’s discussion is not about evolution per se but the distribution of functions across the genomes or extant organisms and so Moran, who has read the literature, is well qualified to comment. Anybody with sufficient background to read and understand the scientific literature on the subject can likewise comment productively.


S. cerevisiae - #66616

December 16th 2011

Your 15% functionality estimate is an argument from ignorance…it is equally an argument from ignorance to say:  “We can’t see any functionality for this DNA at the moment, so we won’t find any in the future, and at best, we will only find functionality for 15% of it.”  No one is in a position to say that.  

PNG didn’t write anything remotely resembling that. Why don’t you address what PNG actually wrote?

James R - #66620

December 16th 2011

S. cerevisiae:

Read PNG’s second paragraph, slowly and carefully.  He did not frame his claim in the way that I did, but he clearly adopted a 15% figure, and that included “a large allowance for future discoveries of function.”   I added the judgment that this conclusion was an argument from ignorance, but the figure was definitely his and I did not try to misrepresent the very clear meaning of his paragraph.  However, my wording was poor.  I should have written:  “We can’t see any functionality for this DNA at the moment, and we don’t expect to find much in the future, and if we do, at best the grand total will be 15”%.”  I hope that clarifies.


S. cerevisiae - #66622

December 16th 2011

Read PNG’s second paragraph, slowly and carefully.

I did. Did you? What do you make of the initial qualifier, “At the moment…”?

He did not frame his claim in the way that I did, but he clearly adopted a 15% figure, and that included “a large allowance for future discoveries of function.”

I wasn’t questioning the 15% figure, which is extremely generous. I was questioning your misrepresentation of his claim.

I added the judgment that this conclusion was an argument from ignorance, but the figure was definitely his and I did not try to misrepresent the very clear meaning of his paragraph.

Calling it an argument from ignorance is a gross misrepresentation of what PNG wrote, particularly given that you’ve unequivocally stated that dogma is wrong and hypotheses have been falsified and confirmed, but you’ve utterly refused to quantitatively support those statements. How did you reach them if you’re only just now working through the book again???

However, my wording was poor.  I should have written:  “We can’t see any functionality for this DNA at the moment, and we don’t expect to find much in the future, and if we do, at best the grand total will be 15”%.”  I hope that clarifies.

No, it’s still a misrepresentation, particularly since PNG allowed for a DOUBLING of the amount of DNA known to be functional. I don’t see the slightest reason for you to reword what PNG wrote, unless…

Hey, but I’m waiting for YOUR numbers or for Wells’s numbers. Where are they? Has Wells documented a doubling with the number of citations that you’ve waved around FOUR times as though it means something (other than that you don’t have any confidence in Wells’s conclusions or your own claims)?

Numbers, James. Numbers…

James R - #66624

December 16th 2011

S. cerevisiae: 

PNG indicated that the 15% was the total AFTER the generous doubling of known functionality.  In other words, he set 15% as probably the maximum, and hinted that the number would likely be lower.  My interpretation of his words is sound.  And what we think we know “at the moment,” given that we are in the midst of a knowledge explosion in the life sciences, is likely be incomplete, confused, and in some cases downright wrong.  So if “at the moment” it looks as if not much of the genome is functional, the proper attitude is caution, not a hasty conclusion that probably no more than 15% will ever reveal any function.

If we assume that even after doubling all known functionality, only 15% of the genome will likely disclose any function, we are unlikely to look for function.  The theoretical justification for such an abandonment of the search for function is a model of evolution which bars any role for design and places high value on contingencies and accidents which constantly clutter up the genome and leave all kinds of rubble lying around which the organism never gets around to jettisoning.  In this view, the genome is analogous to a house with an attic 8 or 9 times bigger than the rest of the rooms combined, filled with old broken rocking horses, moth-eaten wedding dresses, and forgotten 8-track tape players.  Thus, there is a direct relationship between the theoretical model of evolution and the kind of things that scientists are directed to look for in the genome.  Fortunately, there are a still a number of non-ideological biological researchers with healthy empirical instincts who respect a good experiment more than speculation.  It is those people who discover function where the theoreticians have counselled (implicitly if not explicitly) that we should abandon looking for it.

I will reply one more time to PNG, if he responds, because he deserves to hear from me directly rather than through my answers to a somewhat caustic intermediary.  After that, if the thread does not return to the discussion of paradigms, I shall exit.  I do not find this sort of throw-down-the gauntlet form of debating productive.


Argon - #66668

December 18th 2011

James R wrote: “Thus, there is a direct relationship between the theoretical model of evolution and the kind of things that scientists are directed to look for in the genome.  Fortunately, there are a still a number of non-ideological biological researchers with healthy empirical instincts who respect a good experiment more than speculation.  It is those people who discover function where the theoreticians have counselled (implicitly if not explicitly) that we should abandon looking for it.


On the surface that may sound like a good argument but makes some odd assumptions about how researchers actually spend their time trying to understand how organisms operate. The thing is, most researchers aren’t trying to find functions for any randomly chosen segment of an organism’s genome. That’s an undirected search and not often practical, particularly when most research programs are targetted for understanding particular phenomena (like the mechanisms of transcriptional activation or the role of a particular kinase in cancer progression). No, they tend to discover functions and interactions and then trace these back to their sources. Sometimes these interactions map back to the genome and voila, a functional assignment can be made for particular sequences. Maybe even a new class of sequences are characterized. At no point is someone saying: “Well, most of the genome is junk so there is no sense tracing a regulatory function I’ve just discovered to any bit of uncharacterized DNA!!” Basically, the idea that most of a eukaryote’s genome has no specific function does nothing to halt the discovery of previously uncharacterized sequences. The “ideology” of biological researchers doesn’t really play into it.

That said, there are groups who are trying to develop new ways of detecting which randomly chosen segments of the genome may have phenotypic importance. But again, the choice of whether to develop and test these detection methods has little to do with whether one thinks 1% or 99% of the a genome has function, because the work is likely going to pull up interesting new stuff regardless. So far most of the work seems to reinforce previous thought.

James R - #66671

December 18th 2011

Argon:

Thanks for your comments.  You know how to disagree in a gentlemanly fashion, unlike a certain character around here, who is among the “yeast” well-mannered debaters I’ve encountered. 

You make a good point about the natural lines of biological investigation.  I’ll bear your presentation in mind as I read through Wells’s book, as a useful counterpoint to what he is saying. 

Why can’t all ID critics be like you?


James R - #66619

December 16th 2011

S. cerevisiae:

Why would you want a half-baked literature search on the subject of DNA functionality from a generalist like myself, when you can get a full technical treatment, complete with hundreds of citations from the most recent peer-reviewed literature, from Jonathan Wells?

My last detailed reading on the junk DNA question is a while back, so I can’t give you up-to-date figures on the amount of newly discovered functionality.  If you want numbers of the kind you are asking for, read:

Jonathan Wells, The Myth of Junk DNA (Seattle, 2011).

I’m working through it now.  I won’t make any detailed arguments from it until I’ve finished it.  It would be irresponsible for me to do so.

I’m not saying that everything in Wells’s book is absolutely correct (what scientific book is ever absolutely correct?), but this is the most thorough thematic study of “junk DNA” that I know of.  And since Wells has a Ph.D. in biology from a good university, and has studied the subject for probably more than 10 years now, and is a good writer with a knack for explaining difficult scientific concepts to the lay reader, I thought that it might make a good introductory book on the subject for beaglelady.  Even if she doesn’t agree with Wells’s conclusions, she will surely learn a lot from reading the book. 

If you know a better broad scientific study dedicated to the subject of junk DNA, recommend it to me and I will have a look at it.  I’m not committed to the view that everything said by ID proponents is gospel truth, and I’m always open to other positions, provided they are argued with reason and evidence, and avoid ad hominem remarks.  But don’t bother recommending blogs by people like Moran whose desire to destroy ID is well-known.  Blogs aren’t research.  Blogs are places where scientists with too much time on their hands take a holiday from all the rigors of proper scientific discipline, and blow off steam, offering half-baked arguments and nasty ad hominems which they would never dare to submit to a peer-reviewed journal.  Recommend to me a well-researched book written in a civilized tone.


S. cerevisiae - #66621

December 16th 2011

James R,


I didn’t ask for a literature search, so your attempt to attribute that to me is puzzling at best.

You made concrete claims about dogma being wrong hypotheses being falsified in no uncertain terms. The last time you did any reading has zero relevance to your unwillingness to answer simple, concrete questions regarding your claims. Now you claim that you’re just “working through it”? How could you have been so confident in your initial claims? On what evidentiary basis did you make them?

On what page will I find the numbers in Wells’s book? Are you claiming that there is a quantitative answer to my quantitative question in the book?

You’re clearly fudging on the terms “research” and “study” here. In biology, those terms refer to empirical activities, and Wells hasn’t done any in genetics. Larry Moran is an actual geneticist, but you are so eager to prop up Wells that you made an objectively false claim. Note that by challenging your false claim, I am not somehow endorsing his blog, OK?

How can you claim that Wells has a knack for explaining difficult scientific concepts if you are unwilling to discuss those very concepts in any detail or quantitative sense?

Please don’t call Wells’s book a “broad scientific study,” because we both know it’s nothing of the sort. As to your claimed openness, are you open to data, or just to rhetoric? After all, you made clear claims about the data that you are backing away from.

And I think you know that I haven’t recommended any blog. I’ve directly questioned YOUR claims, and you are running away from them.

Wells’s book isn’t research. I recommend real research to you via the peer-reviewed literature that you only seem to be capable of counting. I’m very confident that you won’t take my recommendation to heart.

PNG - #66628

December 16th 2011

“Design theory doesn’t require that all of the genome should be functional.  It’s compatible with the accretion of non-functional elements.  But it would predict that most of the genome, including most of the “noncoding” portion, will have function.”

I don’t see any logical basis for this statement, which was the main point of my post. Why would design theory predict that any specific fraction of the genome would be functional? It seems that design theory says something about the origin of whatever part of the genome is functional, but why it should say anything about how much of the genome is functional is beyond me. For the rest of the post, I was just trying to give some idea of current evidence on how much of the genome is functional, and why we shouldn’t be surprised if a lot of it has no function. There are a number of lines of evidence supporting the idea that a lot of the genome isn’t functional, but my main point is that I can’t see why it should matter to design theory. It’s plain enough that whether or not the genome was in some sense designed, it wasn’t assembled like a machine on an assembly line where any unnecessary bit would be cut out (or never added in the first place.)

If you think that some rough idea of how much of the genome is functional is going to keep scientists from studying it, you haven’t been around scientists very much. They will go on looking for function, and if they don’t find any, they will keep trying to define how it got in it’s current state in more detail. I would guess that if, after several decades, no one can find any function for large parts of the genome, interest (and funding) will taper off. In the meantime, I don’t see how accepting design theory would help the process at all. 


James R - #66629

December 16th 2011

PNG:

You are correct to say that no specific fraction of the genome would be specified by design theory.  But if you suspect that something is designed, and if by design you mean the careful matching of means to ends, parts to the whole, then even if you allow room for some tagalong accretions—even if you build into the original design of the genome some features which will allow useless accretions to be there without damaging function, there are limits on that sort of thing.  I can build a car so that it will run safely with mud on the fender; I can’t build it so that it will run with mud in the fuel tank, or even in the windshield wiper fluid tank.  Most of the parts of a car (taking away the radio, glove box, etc.) are necessary for function, and most of the things one might throw into the engine or interior would impede either the engine or the driver in some way. 

I disagree with this statement:

“It’s plain enough that whether or not the genome was in some sense designed, it wasn’t assembled like a machine on an assembly line where any unnecessary bit would be cut out (or never added in the first place.)”

It’s not plain enough to me.  Or rather, it is plain that it wouldn’t be assembled literally like a car, in the sense of hands mechanically attaching one part to another; but it doesn’t follow that the parts wouldn’t be carefully adjusted with the function of the whole in mind.  And if the parts are carefully adjusted with the function of the whole in mind, there will only be a limited amount of “slack” whereby some things can be left out, and some unnecessary and unrelated things added.

Keep in mind that I have in mind primarily the first genome; it would have nothing but was was necessary for (a) its own function and (b) if we are working within a design-evolutionary model (e.g., Michael Denton), extra bases with no present use but making up “modules” necessary for future evolutionary developments.  After the first genome, you would of course get some disturbances due to mutations, and so eventually there would be built up some extraneous stuff hitching a free ride.  But unless there was some mechanism to keep all that extraneous stuff from interfering with basic organismal functions, there would be trouble.  So one would expect some pruning mechanisms to get rid of a lot of it, or some restraining mechanisms to “quarantine” it somehow.  But “quarantining” ever-increasing amounts of useless material wouldn’t be a wise investment for an organism, so pruning would probably be more likely.  Overall, one would expect most of the DNA to be functional for something.  I can’t give you a percentage.

Now you can respond with:  Look, there is no empirical evidence that most DNA is functional.  I would agree that this counts against design theory.  On the other hand, while the majority of the DNA is still unaccounted for, the fact that new uses keep popping up suggests that the percentage of functional DNA may slowly rise, the more we learn.  I think you as a scientist would agree that we are in the midst of a knowledge explosion in the life sciences, especially in genetics and developmental biology, and that there are going to be many surprises in the decades ahead.  There are still thousands of things we just don’t understand about life.  It might be that things we learn in the next 10 years cause you to revise that 15% estimate considerably upwards.

I’m not pushing design as a dogma.  That would be as bad as pushing neo-Darwinism as a dogma.  I made a very limited point, which is that design theorists would not discourage the search for function.  I could have made it stronger:  they would actively encourage the search for function.

I cannot account for individual psychological makeups.  If the belief that something was designed would make no difference in the way you do science, that is fine, but you can’t speak for everybody.  For some it would an encouragement.  You may think it wouldn’t make much difference, but you don’t have a very good sample to base that opinion on, since design was taboo in biology over your entire working career, and you won’t have encountered enough biologists who believe in design to get a sense of how it affects their habits of inquiry.

We’ve sidetracked far too long on the junk DNA thing.  It was just one illustration out of many that I could have chosen for beaglelady.  Let’s get back to the discussion of paradigms, or else put this thread to a merciful end.


melanogaster - #66881

December 31st 2011

One illustration?


It illustrated that everything you said here about “junk” DNA was either wrong or at best unfounded. Are you proposing that as an example?

For example, you’ve been asked a highly relevant question about your bold, certain statements. On what page(s) of the book did Wells give the proportion of DNA whose status has been changed from nonfunctional to functional?

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