Wednesday, November 03, 2010

Why I changed my mind over macro-evolution?


On 19 February 2009, my friends and I were discussing about macro-evolution, whether is there any evident for it. I told them that I thought macro-evolution theory was correct because of its highly reliable predictive power as seen in the discovery of the Tiktaalik:

"Previous research suggested that vertebrates' invasion of land took place about 375 million years ago in a river — so Shubin and fellow researchers searched for fossils in 375 million year old rocks that had preserved a river delta ecosystem. Having studied other organisms from this water/land transition, the paleontologists knew what sort of animal they were looking for. And when they did discover Tiktaalik (after five separate expeditions to Canada), it wasn't much of a surprise: Tiktaalik had the set of characteristics that they had expected to find in such an organism."
(Emphasis added)

Tiktaalik is considered as the transitional link between fish and tetrapod (creature with backbone and four limbs). Macro-evolution theory postulates that the ancestors of current day land creatures were aquatic. Here's the simplistic description:

Fish-->Tetrapod-->Amphibian-->Land creatures

And the Tiktaalik marks the transitional link between fish and tetrapod in the evolution-chain above. This also means that a tetrapod did not precede the Tiktaalik in the chain in the same way land creatures did not precede amphibians.

However, in January 2010, Evolutionnews.org highlighted a report published in the magazine Nature 463, 40-41 (7 January 2010), that footprints of tetrapod were found. And these footprints dated to about 20 millions year before Tiktaalik's era. This calls into question that the Tiktaalik is the transitional link between fish and tetrapod since tetrapod existed before Tiktaalik.

A few months ago, in June, I read through James Le Fanu's book 'Why Us?: How Science Rediscovered the Mystery of Ourselves'. The book calls into question the prevalent uncritical acceptance and endorsement of the theory of macro-evolution, particular the notion of 'natural selection', based on the scientific discovery in the area of neuroscience, the origin of language, genetics, human anatomy, etc.

One of the arguments made is the problem in our fossil record:

"The problem is that the history of life, as told in the fossil record, reveals the contrary pattern of the sudden emergence (in successive wave) of a diversity of new life forms; their persistence, virtually unchanged, over millions of years; and then their sudden and unexplained disappearance--only for the whole cycle of emergence, stability and extinction to be repeated. Thus, brief synopsis of the 'History of Life' starts three thousand million years ago with those first single-cell organisms. Then nothing much happens till six hundred million years ago with the 'Cambrian explosion' of marine fossils, which culminated in their mass extinction 250 million years later. This was followed by the 'dinosaur explosion' that lasted till their mass extinction seventy million years ago. And this in turn was followed by the 'mammalian explosion' of which we are a part. Meanwhile, along the way the major groups that mark the crucial transitions from sea to land and land to air make their appearance with little or no warning. 'It is as though life goes behind the bushes and emerges in new clothes,' writes the biologist Robert Wesson of Harvard University--and in an abundance of diversity that defied all imagination."
(James Le Fanu, Why Us?: How Science Rediscovered the Mystery of Ourselves [USA: Vintage, 2010), 95-97. Italic original.)

The entire book argues that if we are not sure of the mechanism that enabled the emergence of life, then we should not simply embrace any theories, like natural seletion, that are available in the market and take it as truth. Somethings are meant to be mysterious at this juncture of human discovery.

In the recent exchanges between the Discovery Institute fellows and BioLogos fellows, the matters about the Tiktaalik and those biological explosions in our fossil record were brought up. BioLogos, which propagates macro-evolution theory, mentions the fossil record but neglect the biological explosions. They mention Tiktaalik but neglect the discovery of tetrapod footprints.

It is understandable for their negligence as the neglected matters pose real problems to their interpretation of both the fossil record and Tiktaalik.

I think such approach to the contribution to the deposit of general knowledge, particularly in science, is dishonest. And this is not the first time organizations and individuals that propagates macro-evolution theory neglect these matters in their description of fossil records and Tiktaalik.

There have been other occasions when misrepresentation being made by proponents of macro-evolution theory against those who disagree with them. A recent one is one made by John Wise on Michael Behe.

These made me wonder. If macro-evolution is true, why then the need to provide only half-truth and misrepresentation about the theory and dissenters?

My current agnosticism over macro-evolution is the result of seeing all these misdeeds done by its proponents. In a way, they are worse than the medieval Roman Catholic authority in their dealing with Galileo. At least the Catholics back then did not misrepresent Galileo.

57 comments:

Israel Lee said...

Josh, thanks. I have always struggled with macro-evolution and the almost religious fervency some of its proponents seem to show.

Your posting have allowed me to be more comfortable in doubting the theory. ;-)

Sze Zeng said...

Hi Israel,

I'm glad that the post helps. The sentiment has been growing since early this year when the footprints of tetrapod are found. James Le Fanu's book helps to crystalize the issue.

Israel Lee said...

Some of the reviews on Amazon say that this book is in support of creationists. What do you think?

Sze Zeng said...

In support in the sense by pointing out the problems in macro-evolution theory.

You know the old saying "the enemy of your enemy is your friend"? So it is in support in that sense.

On the book's Acknowledgement page, the author listed both who are for and against macro-evolution, ranging from Keith Ward to Michael Behe to Alister McGrath and Denis Alexander.

Israel Lee said...

You just decided on a trip to Borders for me. ;-)

Sze Zeng said...

By then again, the term "creationist" is dubious.

ID proponents think that everyone who affirm the need for a Creator (includes theistic evolutionist) as the best explanation as "creationist".

Usually theistic evolutionists think that "creationist" reserves to those who are young-earth-creationist.

So it really dubious to use the term "creationist" by the reviewer without clarifying which meaning does he mean.

Sze Zeng said...

Hahahaha... and helped to stimulate the economy by increasing revenue for Borders, shipping company, the publisher, printer, and the author.

Israel Lee said...

Borders lost my sale because they do not have a web presence for stores in Malaysia. So, it is MPH at RM49.90. Might as well since I can get membership points.

Yes, creationist, the label, has been around for a long time and the ID camp normally distant themselves from the young earth-six days-literal creationists. I think this negative association between ID and creationist contribute much to the lost of the court case in the states.

SHWong said...

Joshua, you are throwing the baby out with the bathwater. Evolution as a theory is based on so much more than fossil records.

A more rational response to the discovery of the tetrapod footprints would be to refine the fish-tetrapod transition details. It doesn't falsify the theory. As with most scientific evidences, it improves it. This is why most paleontologists celebrate the find.

Sze Zeng said...

Hi SHWong,

The only material evidents we have to argue for macro-evolution (not evolution per se) is fossil records, as none of us witness any macro-evolution occurring in our lifetime.

How do the footprints of tetrapod refine the transition details? To "Tetrapod-->Fish-->Amphibian-->Land Creatures"

But this poses a serious problem to macro-evolution. As the refinement itself contradicts the claim made by Neil Shubin et al in their discovery of Tiktaalik as the transitional link between fish and tetrapod which was expected.

Even if revision of the chain can be done (which none macro-evolutionists or paleontologists would agree due to abundant evidences in the fossil records--fish fossils are much older than land creatures), there is no positive material evidents to affirm macro-evolution.

Sze Zeng said...

Hi SHWong,

For all that I have said, however, as my stance towards macro-evolution is agnostic, I am still open to it being correct. :)

reasonable said...

As it happened before in Science, there were times when anomalies surfaced that seems to contradict a scientific theory (for others who do not know: theory is a hypothesis that has passed scientific tests and hence established as true until further evidence shows otherwise). The usual approach would be to think of an ad-hoc hypothesis that can reconcile the anomalies with the theory instead of rejecting the theory. Until more and more anomalies surface, or a much better theory (i.e. a better hypothesis that passed scientific tests) comes along, the current theory would not be rejected on account of some anomalies. It ever happened that by inventing an ad-hoc hypothesis (to reconcile anomalies) to keep the main theory, at a later time, the ad-hoc hypothesis itself (which was originally invented to protect the main theory) is proven true. Hence usually scientists do not discard a theory on account of some anomalies, if the theory itself can be supported by many more other tests/data/evidence.

Even if the some tetrapods were found to be around 20 millions years before the discovered Tiktaalick (makes me think of Teh-Talik, haha), it may mean that there was a 20 to 30 million year period of transitional period. The 20 million-year period does not seem to be significant in view of evolutionary timeframe of a few billion years. Hence, could the anomaly be due to the existence of an overlap period between the Tiktaalik-type animals/creatures and tetrapods, while the overall pattern of evolution of
fish --> tetrapods remaining true?

In other words, could it be a case of some tetrapods had already been transformed fully from Tiktaalik-type animals 20 to 30 million years before other tetrapods; meanwhile Some Tiktaalik-type animals had not been transformed into tetrapods yet until another 20 to 30 or even 50 million years later. So in between, over the 20 million to 30 million years.

I know very little about evolutionary studies, and hence the above thoughts about evolution are just my speculations.

Sze Zeng said...

Hi reasonable,

You know that I am in agreement with your description of anomalies in science.

On another hand, there are instances where a scientific theory of the minority was eventually proven true even though at the time of its proposal, it went against the tide of the scientific majority.

These two sides of the coin have to be held on cautiously.

You suggestion is of course a possibility. Meanwhile we still need to wait for further discovery to understand what happened.

(In Malaysia, it spell "Teh-Tarik." Yes, I thought it was weird when I heard for the first time the name Tiktaalik! hahaha)

SHWong said...

Joshua,
Well, I think you are intentionally vague with the word "material evidences". Kindly check out this link where it lists out at least 29 forms of evidences for macro-evolution: http://www.talkorigins.org/faqs/comdesc/

While fossils are the direct remnants of the ancient past, there are still a lot that we can directly infer from existing "materials". For me, the best "proof" of macro-evolution is the nested hierarchies, which is the only form of hierarchy logically and mathematically possible with existing DNAs. Nested hierarchies entails ancestor-descendant relationships. Ancestor-descendant relationships entail macro-evolution. This is only one of the methods of deducing evolution, but a strong one because it is independent of any existing assumptions in biology. It needs only a strong working knowledge of mathematics (statistics).

So while skepticism is a healthy stance in all fields of knowledge (including theology), agnosticism is less so when the evidences lean stronger on one side.

Sze Zeng said...

Hi SHWong,

Thank you for the link. It seems like a decent site to learn about macro-evolution.

However I am current in rush hour and managed only to go through the two websites on phylogenetic, common descent, and 'tree of life'. (http://www.talkorigins.org/faqs/comdesc/phylo.html and http://www.talkorigins.org/faqs/comdesc/section1.html#chronology) And I have found problem in that.

The former website make reference to W. Ford Doolittle's Phylogenetic Classification and the Universal Tree (1999) about "horizontal transfer" as a "caveat" to the phylogenetic tree hypothesis. But surprisingly there is no mention of Doolittle's criticism in the detailed discussion on the latter website.

Here's Doolittle's quote which the website doesn't include and which undermine the argument of phylogenetic:

"Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree."

The passing remark about "convergent evolution" on the first website also poses serious problem to the phylogenetic tree hypothesis.

The website does not recognize the seriousness of how convergent evolution has undermined the idea of 'common descent' or 'tree of life'.

"Certain resemblances are convergent -- that is, the result of independent evolution. We cannot always detect these convergences immediately, and their presence may contradict other similarities, "true homologies" yet to be recognized. Thus, we are obliged to assume at first that, for each character, similar states are homologous, despite knowing that there may be convergence among them."
(Guillaume Lecointre & Hervé Le Guyader, The Tree of Life: A Phylogenetic Classification [Harvard University Press, 2006], 16)

I will look through the rest of the arguments.

Sze Zeng said...

In other words, even among the proponents of macro-evolution, there is no need for the hypothesis of "tree of life", "common ancestor", and nested hierachy. These hypothesis are considered, in a way, redundant if not less strong as a scientific explanation for macro-evolution.

Even the President of American Scientist, Lynn Margulis, thinks so:

"But many biologists claim they know for sure that random mutation (purposeless chance) is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk, dichotomously branching-phylogenetic-tree pattern! "No!" I say.[...] This profound research question is assiduously undermined by the hegemony who flaunt their "correct" solution. Especially dogmatic are those molecular modelers of the "tree of life" who, ignorant of alternative topologies (such as webs), don't study ancestors."
(http://www.americanscientist.org/issues/pub/2006/3/the-phylogenetic-tree-topples)

In another occasion, Margulis said:

"...new mutations don't create new species; they create offspring that are impaired."
(Darry Madden, "UMass Scientist to Lead Debate on Evolutionary Theory," Brattleboro [Vt.] Reformer [Feb 3, 2006]).

SHWong said...

Thanks Joshua for your comments. I appreciate especially the input from Margulis.

I already know about convergent evolution and horizontal transfer. But those are part of the building blocks of the entire evolution theory, not counter-arguments.

Nonetheless, I suspect we are more or less on the same page on our level of confidence on evolution. For me, the current details of the theory will continue to be fine-tuned by people like Margulis, but the entire thing is too well-established to be rejected.

The theory itself is very much different from the original version from Darwin.

Sze Zeng said...

Hi SHWong,

Sorry that I cannot go through the rest of the argument in detail from talkorigins.org as I have two essays and one sermon to prepare. Deadlines are two weeks later.

Darwin's version of the "tree of life" is, as we now know, outdated. Phylogenetic by cladistic hypothesis (common ancestor/descent--tree of life--nested hierachy) as developed by Talkorigins.org is an extremely weak, if not debunked, support for macro-evolution. So I think that any contemporary attempt to argue for macro-evolution cannot be derived from this hypothesis (if I may call it "phylogenetic-claudisticism") until further discovery are found.

To me personally, this would mean that one conventional argument in support of macro-evolution is eliminated.

As scientific knowledge is tentative in nature (which I think both of us agree), this hypothesis might came back to life in the future. But right now, I do not see any merit in it.

Sze Zeng said...

Hi SHWong,

Not sure if you know about Douglas Theobald's (author of talkorigins.org) latest celebrated article published five months ago that applies Bayesian statistics to show UCA hypothesis (Universal Common Ancestry) as much more probably than other hypotheses such as those by convergent theories.

You can read the news here: http://www.sciencedaily.com/releases/2010/05/100512131513.htm

Though some hailed Theobald's article as confirming Darwin's common descent/tree of life theory, he has not shown that the theory is in fact true. What he has shown is that UCA is more probably than other hypotheses to explain macro-evolution.

To give an illustration. Let's say a murder was committed and somehow Simon was caught (an eyewitness nearby the murder scene saw Simon walking around that area which usually no one would go). Simon denied that he was the murderer, and no one know and why how did that murder happened.

At the court, the prosecutor (whose job was to demonstrate that Simon was the murderer) conjectured three theories (A, B, and C) based on available clues (the above mentioned eyewitness and etc). Then the prosecutor applied Bayesian statistics on his theories and found that theory C is much more probable than theory A and B. Then he concluded that theory C is the reason why and how the murder was committed by Simon (whose guiltiness was the basis of the prosecutor's conjectures in the first place).

So does theory C correspond to what really happened at the murder scene? I don't think so. It only shows that theory C is much more probable than the other two theories IF AND ONLY IF Simon is really the murderer.

IMHO, I see parallel in Theobald's work and that of the prosecutor.

SHWong said...

I don't mean to waste more of your time on this, but some of your statements make me unsure if we do agree on some fundamentals of the subject matter. So to clear up any miscommunication:

1. There are no competing theories besides UCA (in academic science). Theobald's work is to use statistics to prove UCA. But it is merely further proof (to show that statistics alone can prove it too). UCA is simply assumed these days and never in doubt.

2. Convergent evolution is part of the entire evolution theory. It is to explain that not all similarities are homologies. Therefore, convergent theories is not a competing hypothesis of UCA. It is another subject matter all together.

3. Phylogenetic by cladistic is still the latest most accepted way to do phylogenetics, so I'm not sure what you mean by "debunked". When evolutionists like Margulis "disagree" with it, they are not saying it is wrong. They are saying that the tree is not 100% accurate because of many other factors like horizontal gene transfer. So the triangle would appear more like a trapezium, since it is a complex state in the beginning. Therefore, if you use her quote but ignore her earlier statement that "From these facts Darwin correctly inferred that life "descended with modification" from common ancestors", you are again throwing the baby out with the bathwater.

Sze Zeng said...

Hi SHWong,

Thank you for seeking clarification. After reading through your list, I have to agree on some and disagree on others.

RE 1) I disagree there is no competing theories besides UCA (in academia science). Convergent theories is one as UCA is "tree of life", convergent is "trees of life."

RE 2) I agree that "Convergent evolution is part of the entire evolution theory. It is to explain that not all similarities are homologies." I disagree that "Therefore, convergent theories is not a competing hypothesis of UCA." How could it not be competing when UCA is argue for a common ancestor, while convergent is argue for common ancestors?

RE 3) It depends on what Margulis meant by "common descents." If she meant it as "tree of life" (UCA), then as she rightly said, the tree has toppled (debunked). If she meant it as "trees of life" (her words "such as webs"), then she was not referring to UCA by "common descents." So I am only throwing the baby out of the water if I confused between both.

The underlying assumption for macro-evolution whether UCA/phylogenetic-cladisticism or convergent is this: same genes detected in different species is evident of common ancestry.

I'm not saying that there is no same genes detected across species. My question is how does this fact (same genes detected across species) necessarily means common ancestry? I am not saying this fact cannot means common ancestry. I am asking does it necessarily means that?

An eyewitness saw Simon nearby the murder scene does qualify certain degree of belief that Simon was the murderer. But to say Simon was in fact the murderer is making a logical leap from possibility to necessity.

Sze Zeng said...

To clarify (RE 2) my perception over the difference between UCA and convergent (see if it makes sense to you):

Both UCA and convergent agree on common ancestry. They disagree on whether common ancestry is universal or not. UCA says, "Yes, it is universal." While convergent says, "No, it is not."

SHWong said...

I agree with common ancestries and trees of life. But these don't disprove UCA, they merely make the tip of the tree really fuzzy (web-like) with interlocking branches.

I disagree with how convergent evolution disprove universality.

My definition of convergent evolution:
http://en.wikipedia.org/wiki/Convergent_evolution

Basically convergent evolution explains how some life can display common traits despite different ancestry. It tells us that they rightfully belong to different part of the tree(s). It used to be a tricky matter based only on observation. These days, analogy and homology issues are easily resolved because we do grouping by cladistics which reduces the odds of mistakes.

Sze Zeng said...

Hi SHWong,

Convergent does not disprove UCA in the same way UCA does not disprove convergent. There are competing theories; competing interpretations over similar observation (same genes across species).

Theobald's latest article shows that by statistics, UCA is more probable than the other competing theories, such as convergent (I have missed this). Therefore Theobald claims that all (hence "universal") species comes from the same common ancestor since by probability UCA is higher than other competing theories.

How does cladistics reduces the odd of mistakes between convergent and UCA? And what 'mistakes'?

(If by cladistics, you mean cladistics by common ancestry [disregarding the difference between common ancestor and ancestors], then yes cladistics support and part of both UCA and convergent.)

Sze Zeng said...

Hi SHWong,

Apologize for a correction:

"Convergent does not disprove UCA in the same way UCA does not disprove convergent. THEY are competing theories; competing interpretations over similar observation (same genes across species)."

SHWong said...

I guess we have to end this discussion because we are talking pass each other. Part of the reason, I suspect, is because we disagree on the definition of convergent evolution. The way I understand convergent evolution means that it cannot possibly be a competing hypothesis of UCA. It is a complementary theory that supports UCA because it explains why lives from different part of the tree can have similar traits. Like why both birds and bats develop wings.

The so-called competing hypotheses refer to "the probability of evolution from multiple, independent ancestors". This is not convergent evolution. E.g. see this phrase from Theobald "Statistically significant
sequence similarity can arise from factors other than common ancestry, such as convergent evolution due to selection, structural constraints on sequence identity, mutation bias, chance, or artefact manufacture." Convergent evolution supports UCA.

Finally, 1 important phrase from Theobald's article:
"Furthermore,UCA does not demand
that the last universal common ancestor was a single organism,in
accord with the traditional evolutionary view that common ancestors of species are groups, not individuals"

In the end, the quibble is really a tiny one for me and in no way affects evolution as a whole. It's only minor disagreements over how wide and complicated it is at the tip of the tree.

Sze Zeng said...

Hi SHWong,

In that case, I agree with you that we disagree on what does convergent evolution means.

You, following Theobald who is a proponent of UCA and whose works dedicated to promote UCA, thinks that convergent evolution as part of ONE same tree.

While I, following Simon Conway Morris whose is currently recognized as the most significant proponent of convergent evolution and whose works dedicate to promote convergent evolution, thinks that convergent evolution is NOT part of the ONE same tree.

"Evolutionary convergence occurs when unrelated organisms evolve similar adaptations to similar environmental or selective pressures, arriving there by very different routes.[...] Our knowledge of animal relationships tells us that neither the common ancestor of molluscs [invertebrates] nor chordates [vertebrates] could possibly have possessed a camera-eye, so quite clearly they have evolved independently [from different trees of life]; the same solution has been arrived at by completely different routes."
(http://www.mapoflife.org/about/convergent_evolution/?section=0)

So it is up to who do we follow when we are defining "convergent evolution". Do we follow those whose research works are not into this area and those whose works are into this area?

It might be a quibble to you. Anyway, I am not so concern over whether is Theobald's UCA better or Morris' convergent. Both of them are not skeptical over macro-evolution, while I am.

Sze Zeng said...

Hi SHWong,

Convergent evolution's version of the tree of life. http://www.mapoflife.org/about/tree_of_life/

"...whilst the groups depicted are agreed to be genuinely ‘monophyletic’ (that is they share a single common ancestor), it should be noted that lateral transfer of genetic material between branches of the metaphorical ‘tree’ frequently occurs at some levels."

This sentence "groups...as genuinely monophyletic" is ambivalent. Can be translated both ways:
1) Each group has its own single common ancestors (plural).
2) All groups share one single common ancestor (singular).

But I guess the introductory part made it clear that it is plural. But I might be wrong on this interpretation. (http://www.mapoflife.org/about/convergent_evolution/?section=0)

SHWong said...

Morris' definition is the same definition as mine, and the same definition as everybody else. I guess I can only say that perhaps it doesn't mean what you think it means, because given that official definition it doesn't contradict nor compete with UCA. (which is why all evolutionists believe in convergent evolution)

I'm must be failing to communicate at some level, so we'll talk this through when we meet.

Sze Zeng said...

Hi SHWong,

Yes, we shall continue this interesting discussion when we meet :)

Actually, not all evolutionists believe in convergent. One example is Stephen Jay Gould who gives three reasons why in his debate with Morris. He ended with a challenge to Morris that human consciousness poses a problem to convergent.

"If complex consciousness has evolved but once in the admittedly limited domain of known evidence, how can anyone defend the inevitability of its convergent evolution?" (http://www.stephenjaygould.org/library/naturalhistory_cambrian.html)

Throughout the debate, convergent is seen as a competing theory.

Rahula said...

Hi Sze Zeng,

I find it strange that you changed your mind over macro-evolution because of some footprints.
Don't you think that you ought "to wait for further discovery to understand what happened" (November 4, 2010 11:33 AM)?

You brought up the issue of misrepresentation. Well, misrepresentations and misquotes by Creationist are plenty and common.
John Wise may have misquoted Behe, but at least it was not misleading. Behe said, "Yes, astrology is in fact one..."

Your blog-article is akin to often quoted fallacious Creationist's question, "But if we evolved from monkeys, why are there still monkeys?

Coming back to the issue of Tiktaalik and tetrapod trackways, again we have a case of Creationist's (Casey Luskin) misrepresentation.

See:
Casey Luskin vs. Reality: The Thundering Climax
http://sensuouscurmudgeon.wordpress.com/2010/09/19/casey-luskin-vs-reality-the-thundering-climax/

See also:
Casey Luskin embarrasses himself again
PZ Myers

The footprint discovery does not change the theory of evolution at all, at least nothing of the sort that would disprove the theory of evolution. It only changes the understanding of the evolution of tetrapod.

I can send you Shubin's and Niedzwiedzki's paper, if you haven't read them. Then, decide for yourself.

Also, note that the find is not supported by fossil bones at the site, and some paleontologists* say they have reservations, because they may have been made by some natural process or other creatures.

* Jeniffer Clack, palaeontology curator at the University Museum of Zoology, University of Cambridge, UK

Philippe Janvier of the National Museum of Natural History in Paris

Edward Daeschler, head of vertebrate zoology at the Academy of Natural Sciences in Philadelphia, Pennsylvania

Robert L. Carroll, a paleontologist at the McGill University’s Redpath Museum in Montreal

Rahula said...

Hi,

Per Ahlberg, Professor of Evolutionary Biology at Uppsala University in Sweden, once said, "I think mainstream science has a duty
and a responsibility to expose creationism and ID for the pseudoscientific frauds that they are." (Evolution and Palaeontology, Interviewed by Paul Newall(2008))

He is one of team members who made the footprint discovery.

Sze Zeng said...

Hi Rahula,

Thank you for your comments.

Yes, my thoughts over macro-evolution has changed. It might change back, but till then, I am content with the fact that there is no way to demonstrate macro-evolution is a fact.

You placed a few names here. Well I am sure you know about the Dissent list collected by Discovery Institute that have names, though minority. But fact is not about numbers.

Rahula said...

Hi,

> You placed a few names here.<

No, I did not, if what you meant was that I collected names of evolution supporters.

Those names I mentioned are scientists (paleontologists) who specialized in fish-amphibian evolution. They are either directly involved with the discovery or have commented on the discovery.

Per Ahlberg, is one of them who made the trackways discovery.

Jennifer Clack is the author of Gaining Ground - The Origin and Evolution of Tetrapods, Indiana University Press, 2002.

Edward Daeschler is one of them who discovered Tiktaalik.

Philippe Janvier wrote an article, Muddy Tetrapod Origins which appeared in the same issue (Nature, January 7) with Ahlberg, Niedzwiedzki, et al's paper.

Robert L. Carroll is the author of Patterns and Processes of Vertebrate Evolution, Cambridge University Press, 1997; and The Rise of Amphibians: 365 Million Years of Evolution, The Johns Hopkins University Press, 2009.

Sze Zeng said...

Hi Rahula,

Precisely these names are those involved in the discovery that the tendency to place high significance in their findings is suspect. These people need grants and recognition to either to continue their job or engage in further projects. (This same rule applies on all sides, those who are for or against macro-evolution)

I am not surprise when scientists talk about how great their works are in proving macro-evolution. Recent one is Douglas Theobald who claims that he has demonstrated universal common ancestry through statistics. But only recently Eugene Koonin disagrees with Theobald's claim.

Rahula said...

Hi Sze Zeng,

Per Ahlberg, is one of them who made the trackways (footprints) discovery. And it is this footprint that made you change your mind.

Neither Per, nor any of those tetrapods experts changed their mind about evolution.

Therefore, I find it strange that you change your mind due to the footprint discovery.

The case of Theobald & Koonin is similar to Tiktaalik & the footprints. Both of them are evolutionists.

I find it strange that while scientist are doing research and publishing their findings, debating their findings etc., Creationists are making definite/final conclusion at every findings.

Regards,
Rahula

Sze Zeng said...

Hi Rahula,

Yes, I'm aware that Ahlberg was the one who discovered the footprints.

As Cornelius Hunter has put it exactly like how evolutionists have been trying to fit their findings according to their theory:

"Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought. So today’s falsification, though it falsifies one of evolution’s most treasured predictions, will be no different."

You wrote: "Creationists are making definite/final conclusion at every findings."

Too general a statement to which I don't really know what is the object of this statement pointing at.

Rahula said...

Hi,

> Too general a statement to which I don't really know what is the object of this statement pointing at.<

An example would be the footprint discovery. Many creationist websites concludes that it proved evolution wrong. The discovery has nothing to do with it at all. Another example would be Koonin's paper.

A better option would be "to wait for further discovery to understand what happened", don't you think?

Rahula said...

Hi,

Cornelius comment could be an oversimplification.

Researchers published their findings and theories in peer reviewed journal, so that their work could be peer-reviewed.

His comment could also be modified and applied to Creationist.

I find it strange that Creationists never made any discovery. Most discovery have been made by evolutionists. I guess they never bother to find out the truth, as they "already know the truth".

Regards,
Rahula

Sze Zeng said...

Hi Rahula,

You asked, "A better option would be "to wait for further discovery to understand what happened", don't you think?"

That's my position. To me, macro-evolution is not an established fact. It is still on going. Just that I go one step further than you in withholding any conclusion in macro-evolution.

http://szezeng.blogspot.com/2010/11/philosophical-exploration-of-evolution.html

You wrote: "Researchers published their findings and theories in peer reviewed journal, so that their work could be peer-reviewed."

It is alright if you have so much faith in peer-reviews. If you want to have so much faith in that, feel free.

http://szezeng.blogspot.com/2010/11/scientific-findings-are-factual.html

http://www.theatlantic.com/magazine/archive/2010/11/lies-damned-lies-and-medical-science/8269/

You wrote, "Cornelius comment could be an oversimplification."

Yes, it is an oversimplification, but is there any elements of truth in it?

If none, than that is simply a false statement. If yes, than Hunter's statement has done its job.

Rahula said...

Hi,


> That's my position. To me, macro-evolution is not an established fact. It is still on going. Just that I go one step further than you in withholding any conclusion in macro-evolution.<

How do you reconcile "waiting for further discovery to understand" with the fact that you have made a conclusion?

> It is alright if you have so much faith in peer-reviews. If you want to have so much faith in that, feel free.<

Ok. But it has nothing to do with faith. It's a critical examination by someone else, usually by qualified individuals within the elevant field.

Well, it is not a surprise that people cheat and tell lies. Even religious people do that - eg. shadow writer, as you yourself said.

With or without religion, you'd have good people doing good things and evil people doing bad things, but for good people to do bad things, it takes religion.

Well, for Cornelius:

"Being a creationist means there is no bad news. If new species appear gradually/abruptly in the fossil record, that just means God create it.
If species then persist for eons with little/significant modification, that just means God is satisfied with His creation / made the modification.
If clever/useless mechanisms are discovered in biology, that just means God is smarter than we imagined......"

You get the idea?

Regards,
Rahula

Sze Zeng said...

Hi Rahula,

You asked, "How do you reconcile "waiting for further discovery to understand" with the fact that you have made a conclusion?"

I don't see there is a need to reconcile as I don't see there is a contradiction in the first place.

You wrote, "Ok. But it has nothing to do with faith. It's a critical examination by someone else, usually by qualified individuals within the elevant field."

Another way to say that is that you have faith in people who you think are reliable. Well, many think that Marc Hauser was reliable too until recently.

And in science, seldom grants are given to conduct experiment or expedition that have already been published. So it is very very fortunate if scientists receive grants to repeat another person's experiments to test it. Usually scientists have faith on other scientists' publication and draw from others' related and not similar experiment for peer-review critical evaluation. Hardly they repeat the entire experiment themselves. With such limitation, hardly people will know if an experiment or expedition.

In Hauser's case, it is because his students were lucky enough to be able to review the video recordings of Hauser's experiments to discover the fraud. But in other cases where no visual recording is archived, the community simply has to have faith on their reporting.

Of course, here I use the word 'faith' to refer to 'trust', and not to something related to established religion.

After quoting Cornelius Hunter, you asked me, "You get the idea?"

I get the sense that you think I am into ID or some sort of creationism. Well, I am not. In the post I referred you to in my previous comment (http://szezeng.blogspot.com/2010/11/philosophical-exploration-of-evolution.html), I have stated there clearly "In fact I'm okay if we don't know how the species around us came to be what they are now. That is I can live without knowing life's origin as in how we came to be."

That means the knowledge of the mechanism of human origin is not important to me. :)

Sze Zeng said...

Hi Rahula,

Sorry for a typo:

"After quoting the edited text of Cornelius Hunter, you asked me, "You get the idea?""

reasonable said...

Rahula, good to see you here again. Sorry I have not gotten down to contacting u via your email.

You borrowed from someone: "With or without religion, you'd have good people doing good things and evil people doing bad things, but for good people to do bad things, it takes religion."

To be more accurate, for good people to do bad things, it takes ideology.

In other words, the ideologies that motivate good people to do bad things could be either religious or non-religious ideology.


Cheers!

Rahula said...

Hi,

Reasonable,

Glad that you still remember me :)
No disagreement with your comments.

What I am trying to say that is that it is not a strange occurence that people cheat and tell lies, and even good people do such things.

Sze Zeng,

> I don't see there is a need to reconcile as I don't see there is a contradiction in the first place.<

How could one make a conclusion if one is still waiting?


> Another way to say that is that you have faith in people who you think are reliable.....<

People who have academic qualification in a certain field. For example, you would expect the physician you see to be qualified or accredited. Having said this, I do not mean others can't give a valid opinion.

>....Marc Hauser....<

That is why research are published in a peer-reviewed journal. I have read many research papers with similar issues, sometimes with different results.
They might not repeat the entire examination, but they might do a similar examination.

Let me give an example, using Hauser as an example.

In 1995, Hauser et al published a paper, "Self-recognition in primates: Phylogeny and the salience of species-typical features". Gallup reviewed the video recordings but could not find any evidence.
Gallup (1997) published a critical response, "Self-recognition in Saguinus? A critical essay". Hauser (2001) reported that his subsequent attempts to replicate the experiments were unsuccessful, observing no evidence for the previously claimed result ("Cotton-top tamarins (Saguinus oedipus) fail to show mirror-guided self-exploration")

> After quoting Cornelius Hunter, you asked me, "You get the idea?"<

Earlier, I wrote (December 28, 2010 12:31 AM):

"His comment could also be modified and applied to Creationist."

I was just doing what I claimed could be done.

> I get the sense that you think I am into ID or some sort of creationism. Well, I am not.<

I must have been mistaken. I am sorry. It's all about the footprint issue, actually. :)

> That means the knowledge of the mechanism of human origin is not important to me.<

Then, I agree with you.:)

Best wishes,
Rahula

Sze Zeng said...

Hi Rahula,

You asked, "How could one make a conclusion if one is still waiting?"

My conclusion is that one has to still wait. Hope this is clearer.

You stated, "For example, you would expect the physician you see to be qualified or accredited."

To me, I see the 'expectation' is an exercise of faith.

My question to your confident expectation in physicians is this: On what basis that you expect them to be right with their prescription and medical advise? You have faith in their certificates and the journals they read? Their certificates and read journals are artefacts to show that they are being well fed with information in medicine.

If it is simply by the virtue that they have certificates and read journals, then it is an act of faith on your part to trust that the information they are fed with is true. Now what if these information that they are fed on is not true?

Do note the previous link I provided (http://www.theatlantic.com/magazine/archive/2010/11/lies-damned-lies-and-medical-science/8269/). It is stated in the article that "as much as 90 percent of the published medical information that doctors rely on is flawed."

You wrote, "I must have been mistaken. I am sorry. It's all about the footprint issue, actually. :)"

I'm actually glad that you initiated this conversation. That certainly help to clarifies myself. Thank you for that. :)

Rahula said...

Hi,

Happy New Year!

> My conclusion is that one has to still wait. Hope this is clearer.<

So, you have not decided about macroevolution?
What type of evidence would you want to have to prove macroevolution?

> To me, I see the 'expectation' is an exercise of faith.<

Yes, but it also depends on the definition of faith. The physicians are trained in medical school, and physicians have been curing people. This does not mean I will not be skeptical of any physicians I am seeing. Doctors are human. Humans make mistakes. One has to be discerning.
Perhaps, one can can call it discerning faith, where doubts are allowed.

> On what basis that you expect them to be right with their prescription and medical advise? <

On the basis of what they do; and the results of their treatment - to myself as well as other patients.

Not all doctors read journals with blind faith. And usually, if research are sponsored by drug companies, it has to be made clear in their research paper.
John Ioannidis' research is also based on science, and published in medical journal. Well, considering most research is flawed, could Ioannidis's research be flawed?

Ioannidis is professor and chairman at the Department of Hygiene and Epidemiology, University of Ioannina School of Medicine as well as tenured adjunct professor at Tufts University School of Medicine and Professor of Medicine and Director of the Stanford Prevention Research Center at Stanford University School of Medicine

Ioannidis predicted "80 percent of non-randomized studies turn out to be wrong, as do 25 percent of supposedly gold-standard randomized trials, and as much as 10 percent of the platinum-standard large randomized trials"


So, 20% is right in a non-randomized studies, 75% in randomized trials, and 90% in large randomized trials?

Sometimes, the question is, would you made a drug that cure 20% of the people suffering from a disease? I know many would agree even if it's only 1%.
I work in the hospital. A drug might work on one person, but not for another 5 person.

By the way, having read Ioannidis' research, would you you still see a doctor if you are sick? If yes, why?


Best wishes,
Rahula


P.S. If you wish to read Ioannidis' research papers, I can send them to you. Both are published in 2005. So, it is nothing new.

He himself served as a member of the editorial board of 26 leading international journals, including PLoS Medicine, Lancet, International Journal of Epidemiology,
Journal of Clinical Epidemiology, Clinical Trials, etc., and has more than 450 peer-reviewed papers.


Why Most Published Research Findings Are False
PLoS Medicine, Volume 2, Issue 8 (August 2005)

Contradicted and Initially Stronger Effects
in Highly Cited Clinical Research
JAMA, July 13, 2005—Vol 294, No. 2

Sze Zeng said...

Hi Rahula,

Happy New Year!

You asked, :So, you have not decided about macroevolution? What type of evidence would you want to have to prove macroevolution?"

My conclusion: Macro-evolution is not established fact. So the jury is still out.

What evidence? I don't know. Perhaps a new species emerges.

You wrote, "Perhaps, one can can call it discerning faith, where doubts are allowed."

That's my point, it's faith, an exercise of trust even without being completely sure or even probably certain.

You wrote, "On the basis of what they do; and the results of their treatment - to myself as well as other patients."

Do you mean before you go to a doctor, you will review ALL of the doctor's past records, interview ALL his/her past patients, and so make a decision to see the doctor based on ALL of these you have done?

You wrote, "Well, considering most research is flawed, could Ioannidis's research be flawed?"

David Freedman who wrote that article I sent to you wrote a book title Wrong. In the book, he asked the same question and tries to answer it.

You asked, "By the way, having read Ioannidis' research, would you still see a doctor if you are sick? If yes, why?"

I think this is a trick question (in the same manner you asked "Well, considering most research is flawed, could Ioannidis's research be flawed?"). You assume that I have a clear answer to all the inconsistency in the society and so I can live without paradox and contradiction. The thing is that I don't, you see.

The fact that I found the society is in a paradoxical and tangled condition doesn't mean I cannot see the paradoxical nature or critique it. By seeing and critiquing doesn't mean I have the better solution. Without better solution, that doesn't mean my critique is therefore not valid. And your question is directed a way that if I say that I go to see doctor, my critique is therefore not valid. But to go there, you have to make many logical leaps that I have highlighted.

Yes, I know Ioannidis' research is published five years ago and nothing new. The thing is that people go around still thinking as if Iannidis' papers do not exist and keep talking how accurate and definite scientific publications are.

Oh yes, please send me Iannidis' articles! Thank you. I'll take that as your New Year gifts to me :)

Rahula said...

Hi,

> Perhaps a new species emerges.<

New species have been observed. I guess we need not go into details, unless if you want to.

> Do you mean before you go to a doctor, you will review ALL of the doctor's past records.....<

On the training they have received. Their teachers were doctors also, so were their teacher's teachers. The "past records" are their training.

> The thing is that people go around still thinking as if Iannidis' papers do not exist and keep talking how accurate and definite scientific publications are.<

Having been an undergraduate and a postgraduate student in health science, we were taught how to do research as well as how to read research papers.
We were taught about the strength and weakness of non-randomized and randomized study. In the practical world, no drug would be made until it has gone through large clinical trials, and sometimes more than one trial.
But research has to start somewhere, and it usually start at non-randomized study. The result is published, so that other researcher may be aware of it, replicate it, review it or critique it. Then, if there is justification, only then it will proceed to a larger trials.
So, Ioannidis's paper does not comes as a surprise.


> Oh yes, please send me Iannidis' articles! <

I have emailed them to you.

Best wishes,
Rahula

PS. It was not a trick question. I asked the question because I initially thought that you don't trust medical science. I agree with your comments/obervation on paradox/contradiction in society (the third last paragraph).

Sze Zeng said...

Hi Rahula,

You wrote, "New species have been observed."

New species have been found which previously not in the database or we observe the emergence of new species in the laboratory? (Given the context of this post is on macro-evolution, so I asking if there is any new macro-evolved species emerged.)

You wrote, "On the training they have received. Their teachers were doctors also, so were their teacher's teachers. The "past records" are their training."

You seem not to get my point that your expectation on the doctors' reliability is an act of faith. Invoking the 'training' doctors received doesn't show that your expectation on their reliability is not based on your *trust* on them. Marc Hauser had training too. So are his supervisors. So if you expectation is simply based on the training they received, then that simply means you trust them because their certificates hanging on their clinic/hospital wall say so.

You wrote, "Ioannidis's paper does not comes as a surprise."

I agree that Ioannidis's paper doesn't come as a surprise. That's not my problem at all. My problem is that his paper just assert how fragile and vurnerable (to an extent, unrealiable) the available methods at determining 'fact' in the current peer-review system. Why I bought Ioannidis up is because you have been describing how confident you are with the current academic system to provide reliable 'facts'. My bringing up Ioannidis is not to say that the unreliability of current system is new. I am just pointing out that your confident in the system seems too ready, as if it is still okay to parade your confident in the system in spite of the fact that you also know that there are problems within the system.

You wrote, "It was not a trick question."

I apologize that I read too much into your question.

Again, many thanks for the papers! :-)

Sze Zeng said...

Hi Rahula,

To explain a bit more:

I wrote, "I am just pointing out that your confident in the system seems too ready, as if it is still okay to parade your confident in the system in spite of the fact that you also know that there are problems within the system."

It seems that you are saying that even though there are problems within the system in doing its job (that is to establish 'facts'), you are still confident in the system.

To me, that's an act of faith. Sounds somewhat (not entirely accurate illustration) like: "I know that Jan Hendrik Schön has flaws, yet I still trust that his works are reliable."

reasonable said...

Hi Rahula,

Can u elaborate on what new animal species have been formed due to macro-evoltion?

"New species have been observed. I guess we need not go into details, unless if you want to."

I briefly came across somewhere that talked about new species of fruitflies being formed under lab conditions. But I also heard objections that it is not an unambiguous case as it could be said that what has been evolved is still fruitflies and not a new species of fruitflies etc.

I have read very little on such things and hence your elaboration would be an convenient way for me (short of time to slowly dig out the right reading materials) to learn :)

Thanks Rahula.

Sze Zeng said...

Hi reasonable,

Talking about fruitflies, check out this piece of news:

"The Science article seeks to show with what amazing rapidity scads of new genes may arise and become essential to an organism. The evidence is from fruit flies.

Two species, D. willistoni and D. melanogaster, diverged starting about 35 million years ago. By comparing genomes, [macro-evolutionist] researchers Manyuan Long et al., showed how "new genetic information can arise quickly, at least on an evolutionary timescale.

Fruit flies are a cherished subject of such investigations because of their rapid reproduction, going from birth to death in thirty days. [...] Fruit flies are supposed to show us how quickly evolution is accomplished. [...] the article may be summarized as follows: 35 million years later, it's still a fruit fly."

http://www.evolutionnews.org/2010/12/praised_be_darwin_do_fruit_fli042131.html

Rahula said...

Hi Sze Zeng,

> You seem not to get my point that your expectation on the doctors' reliability is an act of faith.<

Define faith. Trust on them (their skill, application of knowledge etc), or medical science?
If you defined faith as trust based on "facts" or evidence, then, yes, I have faith in medical science.

Having said this, I hope you do not misinterpret me as saying that medical science understand all diseases and can cure all diseases. Medical science does not make such claim.

Medical science is "facts", research published in peer-reviewed might not be "facts", they are what they are - research.

> Why I bought Ioannidis up is because you have been describing how confident you are with the current academic system to provide reliable 'facts'. <

I guess you still do not understand what peer-reviewed publication is. It does not publish 'facts' only. It publishes research findings of researchers.

I guess I have made this very clear in my previous posting - so that other researchers may be aware of it, review it, debate it, disagree with it, etc.

I have also mentioned that there are different types of research, each with its benefits and pitfalls. Researchers are trained not only to do research, but also how to read research papers.

It is so common to come across a few research papers suggesting the benefit of a certain chemical/pharmaceutical agent, as well as research papers that says otherwise.

No doctors would change their treatment just because of one single non-randomized study. The doctor may use the new treatment as a complementary treatment, with the condition that it is not contraindicated and does not has any side-effects.
The doctor may also conduct his own research.

Of course, being bias and cheating can happen, as in any systems involving human.

-------------

David Klinghoffer's “It’s still a fruit fly” remark is as I already wrote on December 26, 2010 6:23 PM:

".... akin to the often quoted fallacious Creationist's question, "But if we evolved from monkeys, why are there still monkeys?"

Well, the research (Long et al, 2010) shows that microevolutionary processes can produce new genes with modified sequences and new functions, which is clearly new information on anyone’s definition, including Michael Behe’s definition.

reasonable said...

What commonly accepted criteria are there to decide whether or not a newly transformed living thing should be called a new species or merely a variation within an old species?

Rahula said...

Hi,

> what has been evolved is still fruitflies and not a new species of fruitflies etc.<

Well, a new species of fruitflies would still be fruitflies.

If a fruitfly changed into a bird or monkey, that would support the theory of intelligent design.

> Can u elaborate on what new animal species have been formed due to macro-evoltion?<

See:

Macroevolution: Examples and Evidence
http://evolutionlist.blogspot.com/2009/02/macroevolution-examples-and-evidence.html

Observed Instances of Speciation
Joseph Boxhorn
http://www.talkorigins.org/faqs/faq-speciation.html

Speciation
http://en.wikipedia.org/wiki/Speciation

I would also like to specifically mentioned a few papers:

Speciation in the apple maggot fly: a blend of vintages?
Chris Jiggins & Jon Bridle
Trends in Ecology & Evolution (2004), Volume 19, Issue 3, 111-114.

From Micro to Macroevolution Through Quantitative Genetic Variation: Positive Evidence from Field Crickets
Mattieu Begin & Derek Roff
Evolution (2004), 58(10), 2287–2304

Recent Speciation in the Orchard Oriole Group : Divergence of Icterus Spurius Spurius and Icterus Spurius Fuertesi
Baker, JM et al
The Auk (2003), 120 (3): 848-859

Recent Speciation Between the Baltimore Oriole and the Black-Backed Oriole
Kondo, B., Baker, JM, Omland, KE.
The Condor (2004) 106 (3): 674-680

Rahula said...

Hi,

I would also like to point another paper, where the birth of a new species was witness by scientist, at Galapogas Island.:

The secondary contact phase of allopatric speciation in Darwin's finches
Peter R. Grant and B. Rosemary Grant
PNAS (2009) 106 (48):20141-20148