The Evidence for Evolution

The christian youth disagrees with this thread.
Blasphemy.

@spareheadone: lack of common ancestor. This is not what you have posted in the PLoS Biology paper.

As I wrote earlier, in your references they take into account HGT but it doesn't mean they deny the emergence of new species from a common ancestor. Just that point mutations are not the only genetic changes involved. See some of the ref I have posted in my previous comments.

This "web of life" is supported by zero study I could find. There is zero data, zero methods you can analyze. It is the equivalent of a fan-made story.

While I would love to see a paper proving me wrong, as of now, it is just a picture not a scientific graph built following a reproducible method and based on a public data base.

I was just browsing some recent news and came upon the writings of Dan Graur. I never expected an evolutionist to be so candid, yet he is sorely mistaken if he believes his fellows will not find ways to fit ENCODE (project analyzing the human genome) into an evolutionary context. He ironically vastly underestimates the power of imagination:

“if the human genome is indeed devoid of junk DNA as implied by the ENCODE project, then a long, undirected evolutionary process cannot explain the human genome.”- Dan Graur

His solution is of course to kill ENCODE because it is not bearing results he desires. I'm not saying that that is representative of all evolutionists, but it is pretty telling of how it is influenced by the philosophical arena.

On another note, I'm pretty confident that the ENCODE results will be explained away, but right now it's hard to picture how. Whatever way in which it is done, it would be pretty darn difficult to explain even the conservative value of 80% functionality for the genome. Conversely, this fits very well into the Genomic Entropy idea of John Sanford.

@blacklegraph:

It was the "Dud of the gaps" fallacy. If we can't explain it it must be an evolutionary "Dud" ala appendix, tonsils and of course non protein coding DNA.

Is encode still working? Last I knew of them was 5 years ago.

How does genetic entropy fit into it? 20 percent loss of function? I think even if acids do nothing at all they still wait to be recombined into the functionality of the next generation

Exactly. I've always found that pretty odd because many such evolutionists are pretty quick to accuse others of "hindering progress" when an entire aspect of their belief involves declaring things non-functional and not investigating any further. It's a contradiction, but understandable because their theory sort of requires it.

Genetic entropy fits in because if the genome is largely functional as implied, you could almost always expect any change via mutation to be detrimental, a loss of genetic information, or at most neutral. Mind you, that is a conservative estimate, as it is implied that much more than that is functional.

Sanford calculated that with present mutational rates and the measured effects of those mutations, the human genome would completely deteriorate in less than a million years. Therefore, "long undirected evolutionary processes" as described would only serve to kill off creatures eventually, barring any temporary benefits. It is as Graur basically implies: it would be virtually impossible for the human genome to have come about by such means.

No.

This is a factual misrepresentation. On several levels.

1) This is not recent news (2013, that's four years ago)

2) Dan Graur, a respected but now retired (I think) professor never tried to kill the gigantic consortium that is ENCODE and ENCODE is still alive and kicking

3) There was no philosophical bias in his critics

4) There is zero ref to any of your claims

5) Nothing in the ENCODE papers or Dan Graur comments goes against how and what is Evolution, it is just another situation (like the integration of the horizontal gene transfer (see posts above on this matter) , or the use of more and more house-keeping genes and more and more evolved software sto generate phylogenetic trees (see all the posts above on this subject)), where new scientific advances are integrated to the current knowledge.

So, if we go back to the facts: Dan Graur disagreed (and it is his right and several other scientists agreed with his main comments) on several definitions used by ENCODE authors, as they could be associated with an over-interpretation of the data presented in the majors studies published in 2013 by ENCODE.

The core of the disagreement what: what is a functional gene? What is a function? Etc...

Below the ref of these critics, and the abstract of the scientific paper presenting the arguments (Published in Mol Biol Evol).

See also a follow-up of the controversy published in Nature including this sentence from ENCODE main author:

Kellis says that ENCODE isn't backing away from anything. The 80% claim, he says, was misunderstood and misreported. Roughly that proportion of the genome might be biochemically active, he explains, but some of that activity is undoubtedly meaningless, leaving unanswered the question of how much of it is really 'functional'.

Everybody can read the raw material below. Nothing is hidden or suggested or inferred.

Overall thanks to @blacklegraph and @spareheadone to reminding me (and us) this controversy, that show how fun science can be as it is always evolving.

Genome Biol Evol. 2013;5(3):578-90. doi: 10.1093/gbe/evt028.

On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE.

Graur D¹, Zheng Y, Price N, Azevedo RB, Zufall RA, Elhaik E.

Author information

1

Department of Biology and Biochemistry, University of Houston, TX, USA. dgraur@uh.edu

Abstract

A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

ENCODE debate revived online

Nature 509, 137 (08 May 2014) doi:10.1038/509137e

In the social-media age, scientific disagreements can quickly become public — and vitriolic. A report from the ENCODE (Encyclopedia of DNA Elements) Project consortium proposes a framework for quantifying the functional parts of the human genome. It follows a controversial 2012 Nature paper by the same group that concluded that 80% of the genome is biochemically functional (Nature489, 57–74; 2012). Dan Graur, who studies molecular evolutionary bioinformatics at the University of Houston in Texas and is a vocal ENCODE critic, weighed in on this latest report. ENCODE's “stupid claims” from 2012 have finally come to back to “bite them in the proverbial junk”, Graur wrote on his blog. The targets noticed. “Some people seek attention through hyperbole and mockery,” says the report's first author Manolis Kellis, a computer scientist at the Massachusetts Institute of Technology in Cambridge. “We should stay focused on the issues.”

This is just the latest skirmish in an ongoing battle. In a scathing 2013 article, Graur and co-authors argued that the ENCODE researchers had essentially ignored evolutionary evidence that suggests that only 2–15% of the genome was under pressure from natural selection (D. Graur et al. Genome Biol. Evol.5, 578–590; 2013). Graur's paper ended with a bang: “The ENCODE results were predicted by one of its lead authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.”

The latest ENCODE report drew wide attention on Twitter. The paper didn't provide any estimates about the proportion of the human genome that is functional; instead, it laid out the case that any accurate inventory of the functional parts of the genome must include evolutionary, genetic and biochemical data.

Given the history, some Twitter users wondered how Graur would respond. He soon ended the suspense with a series of tweets blasting ENCODE's statistics and methodology. In one, he wrote that “the recent half-hearted recantation of #ENCODE was published without a press release.” In his blog post, he wondered why the ENCODE consortium seemed so eager to back away from its “80%” claim. Through it all, he admittedly showed very little tact. “I believe science is a search for the truth, not a lesson in manners,” he says. “I don't do politeness.”

Kellis says that ENCODE isn't backing away from anything. The 80% claim, he says, was misunderstood and misreported. Roughly that proportion of the genome might be biochemically active, he explains, but some of that activity is undoubtedly meaningless, leaving unanswered the question of how much of it is really 'functional'. Kellis also argues that focusing on the portion of the genome that is shaped by natural selection can be misleading. For example, he says, genes that cause Alzheimer's disease or other late-in-life disorders may be largely immune to evolutionary pressure, but they are still definitely functional.

Lol. You clearly don't know what "factual" means.

1.) The age of the statement is irrelevant to the fact that Graur said it.

2.) Lol. You have to be kidding. From his own twitter page: "My next lecture on the "Kill #ENCODE tour." I didn't say it was cancelled either. I don't know where you got that from. It may not be deliberate, but that just reinforces images of your dishonesty (I'd assume you said he didn't want to kill it out of ignorance...which should make one wonder just how many of your claims are spurious and baseless.)

Kill #ENCODE

3.) Another lol: You think there was no philosophical basis from a self described: A Very Angry Evolutionary Biologist, a Very Angry Liberal, and an Even Angrier Art Lover? Wut in tarnation? Or in his own words: "What ENCODE researchersdid not take into account is that everything is shaped by evolution." You think someone so invested in evolution will not have words to say about results that threaten that belief?

4.) That's what the Internet is for bucko. Neither does having no references have any bearing on the factual matter of the claim. One would think you'd be over that nonsense by now.

5.) Omg. You can't be serious. Nothing in the ENCODE results threatens what evolution is, yet Graur definitely seems to believe that the results do threaten evolution has they imply that it couldn't be responsible for the human genome. I mean, how much clearer do you want Graur's statement to be?

The core of the disagreement obviously goes beyond that because Graur insists that the vast majority of the genome must be non-functional, so regardless of how one defines "function", he would not accept any other answer. It also reveals a backwards approach to understanding the genome. The only reason why Graur holds that the default position is that there is no function is because that is what fits in to his evolutionary assumptions. That also indicates that he would be willing to twist the definition of "function" whichever way he sees fit to preserve that conclusion.

I mean, who can even pretend to not see the obvious bias Graur shows, especially with a title like "the evolution-free gospel?" Basically, it should be obvious to anyone without blinders on that what we have here is a scientist that wants his beliefs to determine the evidence, that would reject results contradicting his opinions on philosophical grounds.

Or in the words of the reporter of said controversy:

Graur’s atheism inflamed his anger at ENCODE. He perceives an echo of intelligent design in the consortium’s "80% claim," which he takes to imply that most of the genome exists because it serves a purpose. "What ENCODE researchers did not take into account," he contends, "is that everything is shaped by evolution." And evolution is slow to weed out useless features. Genetic mutations — the drivers of evolution — occur at random, and those that are deleterious are weeded out, sometimes over many generations. Other mutations, salubrious and inconsequential alike, get passed down to progeny. As a result, species like humans and elephants that have a small effective population size are expected to accumulate a lot of junk in their genomes.

http://science.sciencemag.org/content/343/6177/1306.summary

@blacklegraph: No. You are posting non-stop speculations and try to make them pass for science. I posted the scientific ref behind Graur critics. Then the follow-up summary of the controversy from Nature. The heart of the discord is not atheism vs intelligent design but how dangerous it is to play with biological definitions in order to increase the impact of a work. I'm posting below in a spoiler block the full ref from the Science Article you cite in your comment. It is not a scientific article. Just a speculative one.

I stand by all my comments from my previous post. There are now three ref explaining the context of your post (Number 853). It was pure manipulation on your part.

This is a thread about evolution and this controversy just show how interesting and fast moving is the field of DNA sequencing. So I sincerely thank you again for reminding me and others this episode.

I'll post in my next comment a new example, just coming out today, underlying this even more.

(P.S: and when you write "I read a recent news" when it is in fact a 4-5 years old controversy, yes, it is a factual misconception. And when confronted with it your answer is: "The age of the statement is irrelevant to the fact that Graur said it." you just deflect the fact that you were caught, once again, in the middle of one of your lies)

For once, I just read about evolution, not in a scientific journal but through headlines in the general news that caught my eyes.

See below the titles (and links if you click on the titles) for the general public, and then the ref and abstract of the study itself and finally the updated phylogenetic tree build with DNA extracted from a fossil (how awesome is that??)

DNA solves ancient animal riddle that Darwin couldn't

CNN - ‎5 hours ago‎A previous study tried to place Macrauchenia on the tree of life by using ancient collagen. The new study, led by MacPhee and Hofreiter, built on the 2015 collagen study by extracting mitochondrial DNA from a fossil found in South America. The ...

DNA Solves 200-Year-Old Mystery of Weird Ice Age Creature

Live Science - ‎3 hours ago‎The Macrauchenia genus has puzzled scientists since Charles Darwin discovered limb bones and vertebrae fossils "of some very large animal" in Patagonia and fancied it to be a mastodon, as he wrote in a letter to his mentor, the naturalist John Stevens ...

Scientists recover ancient DNA from a bizarre Ice Age mammal that stumped Darwin and discover it is related to ...

Daily Mail - ‎5 hours ago‎For the first time, scientists have recovered ancient DNA from one of the more puzzling species to have lived during the last ice age, Macrauchenia patachonica (artist's impression). The DNA allows researchers to finally map the mammal's relationships ...

Scientists Use Ancient DNA to Identify Bizarre Species That Baffled Darwin

Gizmodo - ‎5 hours ago‎The species, called the Macrauchenia patachonica, that went extinct around 10,000 years ago and was found in South America, is genetically closest to the order containing the odd-toed ungulates that includes tapirs, rhinos and horses. But finding the ...

Article | OPEN

A mitogenomic timetree for Darwin’s enigmatic South American mammal Macrauchenia patachonica

• Michael Westbury
• , Sina Baleka
• , Axel Barlow
• , Stefanie Hartmann
• , Johanna L.A. Paijmans
• , Alejandro Kramarz
• , Analía M Forasiepi
• , Mariano Bond
• , Javier N. Gelfo
• , Marcelo A. Reguero
• , Patricio López-Mendoza
• , Matias Taglioretti
• , Fernando Scaglia
• , Andrés Rinderknecht
• , Washington Jones
• , Francisco Mena
• , Guillaume Billet
• , Christian de Muizon
• , José Luis Aguilar
• , Ross D.E. MacPhee
• & Michael Hofreiter

• Nature Communications 8, Article number: 15951 (2017)
• doi:10.1038/ncomms15951
• Download Citation
• • Palaeontology
  • Phylogenetics
  • Taxonomy

Received:

01 February 2017

Accepted:

12 May 2017

Published online:

27 June 2017

Abstract

The unusual mix of morphological traits displayed by extinct South American native ungulates (SANUs) confounded both Charles Darwin, who first discovered them, and Richard Owen, who tried to resolve their relationships. Here we report an almost complete mitochondrial genome for the litoptern Macrauchenia. Our dated phylogenetic tree places Macrauchenia as sister to Perissodactyla, but close to the radiation of major lineages within Laurasiatheria. This position is consistent with a divergence estimate of ∼66 Ma (95% credibility interval, 56.64–77.83 Ma) obtained for the split between Macraucheniaand other Panperissodactyla. Combined with their morphological distinctiveness, this evidence supports the positioning of Litopterna (possibly in company with other SANU groups) as a separate order within Laurasiatheria. We also show that, when using strict criteria, extinct taxa marked by deep divergence times and a lack of close living relatives may still be amenable to palaeogenomic analysis through iterative mapping against more distant relatives.

Legend: Posterior probabilities and bootstrap values are indicated on the tree branches. The purple node bar represents the 95% CI for the Panperissodactyla clade divergence date based on the combination of all four calibrations used in this study. Scale bar represents time in millions of years. Grey vertical lines represent five million year intervals.

Communication Systems in the Cell

https://m.phys.org/news/2017-04-genetic-code-context.html

http://m.pnas.org/content/114/18/4745

A codon is a triplet of three nucleotides in DNA. Genes are read in these triplet codons, each one standing for an amino acid or a “punctuation” mark as the gene gets translated. 61 of the 64 possible triplets actually code for amino acids; the others work as “start” and “stop” codons.

Now it is believed that rather than just three nucleotides affecting individual amino acid formation it is actually 3 lots of 3.

The authors of the PNAS paper, Hughes and Chevance, describe what drove them to examine the context for each triplet codon. They were playing with the genes for a component of the bacterial flagellum named FlgM when they noticed something interesting:

Changing the codon on one side of the defective codon resulted in a 10-fold increase in FlgM protein activity. Changing the codon on the other side resulted in a 20-fold decrease. And the two changes together produced a 35-fold increase. “We realized that these two codons, although separated by a codon, were talking to each other,” Hughes says. “The effective code might be a triplet of triplets.”

@spareheadone: nice

What this means? 9 nucleotides get translated into 1 peptide?

@mortein: non. More that 3 nucleotides can be translated in different ways and that in addition you can have post translational modifications etc...

The more we know about biology the more we realize how complex (and beautiful in my opinion) it is.

Agreed. While I'm more of a physics guy, some areas of biology are just amazing to me. Even just the process of natural selection + self-replicating organisms is so powerful that we now use it regularly in many fields of engineering and design. And, things like the workings of the brain are so complex and interesting, that I think we'll be learning from it for a very long time. Biology is like a bottomless well of interesting stuff for us to study and learn from.

Interesting (and short) video about Trilobites

Is there any validity behind the idea that ancient remnants of viruses in our DNA which infected us millions of years ago, are the driving factor of aging today?

@mortein: do you have a ref for that?

I don't remember reading anything about it and the concept seems hard to believe to me as it would suggest that species not infected by these viruses don't age?

So all mammals, birds and others have been infected by the same ones? These viruses all have the same affect on all these different species? If this infection occurred X millions years ago, all these species were not aging before?

Again, I have not read the study behind this, but it seems that it is closer to a Science Fiction concept than anything else...

Edit: a recent work on aging if you are interested by this topic:

http://science.sciencemag.org/content/355/6331/1312

Summary of the paper in Time:

https://www.google.com/amp/amp.timeinc.net/time/4711023/how-to-keep-your-dna-from-aging/%3fsource=dam#ampshare=http://time.com/4711023/how-to-keep-your-dna-from-aging/

This hypothesis is new for me, I found about it this morning, from that video I have posted.

Start at 14:50 is you don't want to watch the entire video.

I guess the idea is that we are all infected by remnants of thousands of ancient viruses, so it's not necessary for all the species to be infected by exactly the same ones, especially since aging effects almost everything, and different species age at different rate.

Andrei Gudkov seems to be a smart and respectable scientist, so it's worth looking into this.

https://www.roswellpark.edu/andrei-gudkov

Thanks for the article,I've been following closely what they are doing with NAD+, so this should be a fun read for me.

I've heard the human trials with NAD+ boosters should start soon, what do you expect the result will be?

@mortein: honestly, I'm glad the FDA exists. I do not consider aging as a disease so any work on this field should look+++ for any side effect. Mice studies will not give you that.

I'm not even sure how to measure the cost benefits of a drug like that. Let's say you preserve some organs from aging but you lose some social ability in the balance? How do you predict that? I'm a physician, my goal is to treat diseases not to give drugs to healthy subjects. So yes, I'm glad that a regulatory system like the FDA exists to control all that.

I don't know if aging should be classify as a disease or not, but it's a fact that aging is bad for you, and that it's potentially amenable to medical intervention.

So what is you opinion on preventative medicine?

@mortein: preventing a disease is always better than to be in a situation where you have to treat one. One of my area of research is vaccine development.

If our life expectancy can increase not only by preventing/treating diseases but also because we find a way to preserve our organs AND cognitive functions longer that would be great. At this stage of drug development, as I told you, I'm worried about the side effects.

A bad comparison, but with some similarities anyway using the muscle and not aging: ok for a drug to treat a myodystrophy (a genetic muscular disease), ok for combining a healthy way of life and exercise to improve you sport performances; but what about steroids to increase your muscular mass? There are side effects as you know.

Anyway, I will try to read about your initial post (insertion of viral DNA in our genome and impact on aging) and come back to you once I read a little bit about it. It should be easy now that you have also posted the ref of the scientist. Not sure when I will have the time for that, but I will definitely do it.

@christovgrigori:

Do you believe in the whole evolution story where an inexplicable biological life form is the common ancestor of all current biological life forms on earth?

@christovgrigori:

so that's a yes but no

Oh my. I can't believe I missed this.

Anyway, the only one throwing speculations here (and not just that, but calling them "fact" as well) is you.

Lol. Yeah, the issue is what Graur says it is.....not his fear for what the results of a study imply for his Darwinian faith, regardless of what his co-workers reveal. Cute.

Omg. I know you said English is your second language, but if that were truly the case you would refrain from speaking as if your grasp of English were perfect seeing as the most common issue you have is misunderstanding what is typed.

I said that I was browsing some recent news when I came upon Graur's work. That led me to the controversy, but I didn't say that the controversy itself was recent. Please refrain from stating anything is a misconception when you cannot even grasp simple English, or at least ask for it to be explained to you if you do not comprehend.

@blacklegraph: read the three refs. The controversy was not about Intelligent Design vs Evolution but about the interpretation or the definition of a "functional genome". This is clearly stated several times. The way you presented this controversy was manipulative at best. Pure lie in my opinion. That's why I posted the three refs. Everybody can access the raw material. As usual you tried to use flood and words to hide the facts. Bad luck, everything is open here.

If you have any reminder of intellectual integrity or honor, you should apologize and delete your initial post.

Again, just because someone states the controversy is "x" doesn't mean it is when their motivations are plain as day.

"Graur’s atheism inflamed his anger at ENCODE. He perceives an echo of intelligent design in the consortium’s "80% claim," which he takes to imply that most of the genome exists because it serves a purpose. "What ENCODE researchers did not take into account," he contends, "is that everything is shaped by evolution." And evolution is slow to weed out useless features. Genetic mutations — the drivers of evolution — occur at random, and those that are deleterious are weeded out, sometimes over many generations. Other mutations, salubrious and inconsequential alike, get passed down to progeny. As a result, species like humans and elephants that have a small effective population size are expected to accumulate a lot of junk in their genomes."

Of course he wouldn't come out and plainly say that. He'd rather go for something like the definition of function because that is a way to bypass the argument. If one redefines "function" as whatever they want, then they can deny the obvious because it threatens their views and implies an "evolution-free gospel." For Graur, "function" must obviously fit in with evolution, otherwise it threatens it. His presuppositions determine the evidence, not the other way around. His very position as what should count as the null hypothesis is based on his Darwinian ideas.

These are conclusions from his co-workers and his own words. What I would consider dishonest is anyone who pretends not to see that. I mean, his twitter page is public, and if definitions were his only issue, he would not be tweeting kill #ENCODE. His crusade against it is obviously personally motivated.

What would deleting original posts accomplish? I certainly don't want you to delete any of yours because they are a clear sign of your dishonesty and inability to argue a point. Now that you mention it though, I guess I may have to go back and make sure you didn't delete anything...

@blacklegraph: again, read the three refs. If you can not see the general context of your citations, I will help you in my next post. I may do it anyway, as I suspect you are doing this on purpose. This is in line with my suggestion that you should delete your initial post. I maintain that it was misleading at best. And a pure lie in my opinion. You should apologize.

Thanks, very interesting. This is a full area of research (aging) that I know next to nothing about. I never heard about this journal (Aging), but I went quickly though it. This is very good science with very strong articles. Are you working in this field? (or a field related to it?).

I've got no formal education in biology, beyond high school, but I've been studying it in my spare time over the last 4-5 years, so I probably know more than your average layman. I was especially interested in the biology of aging, given how this field seems to be growing at the exponential rate over the last 10 years, and if we manage to develop these anti-aging technologies, they will have the potential to transform our lives and society more than anything before them.

Now I'm considering to actually go back to the university and start studying biology, but that won't be an easy path.

AHAHAHAHAHAHAHA!

YES!

I just avoided wasting 30' writing a comprehensive answer on this subject.

AHAHAHAHAHA!

Why didn't you say before that your source of information was the Discovery Institute?

AHAHAHAHAHAH

Link to the "news" from June 21 2017 that you used in your post (No 853)

https://evolutionnews.org/2017/06/dan-graur-darwins-reactionary/

From the journal Evolution News & Science Today knowing that...The articles published at Evolution News are copyright by Discovery Institut

https://evolutionnews.org/about/

So when I first interacted with you (post 634) about your claim that "Evolution is a heavily philosophically influenced field" (post 632), I was interacting with someone from a cult?

AHAHAHAH

I was asking you again, again and again for scientific ref about this particular claim (about "Evolution being a heavily philosophically influenced field") and when finally you give one (post 853, where you wrote "I'm not saying that that is representative of all evolutionists, but it is pretty telling of how it is influenced by the philosophical arena.") it's from the Discovery Institute???

Ahahahahaha

Wikipedia has its weaknesses, but it can also be useful.

https://en.wikipedia.org/wiki/Discovery_Institute

No wonder why you never admit that you lie or that you are wrong. It's probably part of your training.

Are you a recruiter?

That would explain why most of your posts are around Evolution and Religions related threads.

Are you successful at recruiting among comics reader?

Good attitude!

Good luck if you go back to your studies, because you will need a lot a work before being able to work on a specific field of interest. And you won't be paid a lot (if anything) during a long period of time: master student, then PhD student, then fellow...

But if you are really into it, I do think it is worth the journey.

Back to science. An interesting article from last year about the use of evolution and phylogenetic trees to predict microbial traits:

ISME J. 2016 Apr;10(4):959-67. doi: 10.1038/ismej.2015.171.

Predicting microbial traits with phylogenies.

Goberna M1, Verdú M1.

Author information

Abstract

Phylogeny reflects genetic and phenotypic traits in Bacteria and Archaea. The phylogenetic conservatism of microbial traits has prompted the application of phylogeny-based algorithms to predict unknown trait values of extant taxa based on the traits of their evolutionary relatives to estimate, for instance, rRNA gene copy numbers, gene contents or tolerance to abiotic conditions. Unlike the 'macrobial' world, microbialecologists face scenarios potentially compromising the accuracy of trait reconstruction methods, as, for example, extremely large phylogeniesand limited information on the traits of interest. We review 990 bacterial and archaeal traits from the literature and support that phylogenetic trait conservatism is widespread through the tree of life, while revealing that it is generally weak for ecologically relevant phenotypic traits and high for genetically complex traits. We then perform a simulation exercise to assess the accuracy of phylogeny-based trait predictions in common scenarios faced by microbial ecologists. Our simulations show that ca. 60% of the variation in phylogeny-based trait predictions depends on the magnitude of the trait conservatism, the number of species in the tree, the proportion of species with unknown trait values and the mean distance in the tree to the nearest neighbour with a known trait value. Results are similar for both binary and continuous traits. We discuss these results under the light of the reviewed traits and provide recommendations for the use of phylogeny-based trait predictions for microbial ecologists.

Apologize for what? Posting Graur's own words? Lol.

Also lol at the thought that I would not have already read the initial articles. They do nothing to help your denial at all.

Another big LOOOOOOOOOL!!!

What does the Discovery Institute have to do with anything? Is it because their ideological bias is different from yours? You even had the nerve to deny that philosophical influence has nothing to do with people's positions when Graur is the perfect example. In case you missed it, I'll requote it one more time:

"Graur’s atheism inflamed his anger at ENCODE."

I don't know how a statement could be anymore clear. Graur has issues with ENCODE because it threatens one of the core beliefs in his atheism. Also, it's pretty ridiculous to believe that such a veiled ad hominem will help you save face.

You seem pretty adamant about apologies and retractions, yet you are yet to delete the article you posted on sclaed plumage (post 646), or the idiotic one on gene transfer somehow proving genetic change from scratch (post 784).

Lol. What would I be recruiting people for? I'm just here to expose blatant deceptions and encourage people to dust off their brains and use them (let's not forget that you boldly supported willpayton who said that birds evolving from dinosaurs is a fact, and could not back it up except for an irrelevant article on scale plumage.)

Let's also not forget that the greatest fraud in science is related to evolution and several other frauds, deceptions, myths and embellishments have been peddled (with some even in the present day, like the "junk DNA" myth) and are still being peddled today.

And what frauds, deceptions, and myths are you talking about?

@willpayton:

I'm guessing @blacklegraph: is talking about Piltdown man and Haekles embryo illustrations. They would be the most fraudulent examples I can think of.

Frauds are everywhere

@blacklegraph:

1) why would you try to recruit people to your cult?

-Well usually it's for the money.

2) what the Discovery Institute has to do with anything?

-At my level? Once I found out yesterday that you were related to them it explained your attitude

-Legally? It's a proven fraud that has been condemned for using pseudoscience to advance their personal agenda, mostly by creating false controversies where there were none to confuse people.

So basically what you are doing.

@spareheadone: I agree that fraud is everywhere (in science, in finance, in architecture, in sport, in politics etc...). This is human nature. But be careful when you respond for @blacklegraph, it might seem like you defend him. Usually it's not a problem when a viner defend another one, but he has inadvertently exposed himself yesterday as part of a cult, and you may not want to be associated with him.

@bullpr:

Which cult?

@spareheadone: The Discovery Institute itself or one of the cults associated with it. See posts 884 and 891. You can find a lot of information online on the main cult behind the Discovery Institute.

Very nice study showing how the frogs evolved in a favorable way after the asteroid stroked Earth 66 millions years ago.

See below the non scientific article then the ref of the paper with the abstract and the main data.

How a Massive Asteroid Strike Helped Frogs Inherit the Earth

Yesterday 10:35am

Filed to: FROGSPLOSION

• FROGS
• AMPHIBIANS
• FROG EVOLUTION
• DINOSAURS
• DINOSAUR EXTINCTION
• ASTEROIDS
• ECOLOGY
• SCIENCE

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Frogs have been around for nearly 200 million years, but it wasn’t until a 10-mile-wide asteroid struck our planet, wiping out three-quarters of all life on Earth—including the dinosaurs—that these crafty amphibians were able to make their big evolutionary move, according to new research.

A study published in Proceedings of the National Academy of Sciences this week shows that frog populations exploded after the Cretaceous-Paleogene extinction event some 66 million years ago. The sudden disappearance of the dinosaurs, followed by the re-emergence of abandoned ecosystems, allowed frogs to flourish and diversify, leading to the thousands of species that still inhabit our planet.

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Mass extinction events are like giant reset buttons. When a large asteroid struck the Yucatan Peninsula some 66 million years ago, it set off a chain of geologic and atmospheric events that wiped out 75 percent of life on Earth, including nearly every animal larger than 55 pounds (except some turtles and crocodiles). With the giant lizards suddenly gone, and as the environment slowly healed itself, the survivors jockeyed for position within the re-emerging ecosystems. New research from the Florida Museum of Natural History and Sun Yat-Sen University in Guangzhou, China, shows that frogs were among the greatest beneficiaries of the transition from the Late Cretaceous to the post-dinosaur Paleogene.

In an effort to learn more about frog evolution, researchers David Blackburn and Peng Zhang put together a new phylogenetic tree of these amphibians (phylogenetic trees are like family trees, but at the species level, and driven by genetic data) . The researchers looked at 95 genes from the DNA of 156 frog species to establish genetic relationships and develop evolutionary timelines.

Contrary to conventional thinking, Blackburn and Zhang found that most modern frog families didn’t originate during the Mesozoic era—that vast expanse of time during which the dinosaurs reigned. Frogs first emerged hundreds of millions of years ago, but it wasn’t until after the demise of the dinosaurs that their populations really took off. With their lizard cousins gone, frogs became among the most diverse groups of vertebrates, accounting for more than 6,700 known species. As the new research shows, 88 percent of frog species are descended from three main lineages —hyloidea, microhylidae and the natatanura—that emerged during the transition from the Cretaceous to the Paleogene.

Repressed for millions of years, these wiley amphibians were suddenly able to occupy and thrive within vacant ecological niches. The asteroid that struck the Earth, and ensuing environmental changes, destroyed a significant fraction of our planet’s vegetation, but as forests recovered, frogs were one of the many animals groups (mammals included) that were able to take advantage of the new habitats.

The Sixth Mass Extinction Will Be Like Nothing In Earth's History

The sixth mass extinction—the one that seven billion humans are doing their darnedest to trigger at …

Sadly, we are in the midst of another mass extinction event, one of our making. Frogs are threatened like never before, owing to habitat loss, pollution, disease, and other factors. According to the IUCN, nearly one-third of the world’s amphibians are now threatened or have recently become extinct. Frogs managed to survive the dinosaur era, but they’re having a hell of time dealing with us humans.

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

1. Yan-Jie Feng^a,
2. David C. Blackburn^b,
3. Dan Liang^a,
4. David M. Hillis^c,
5. David B. Wake^d,¹,
6. David C. Cannatella^c,¹, and
7. Peng Zhang^a,¹

Significance

Frogs are the dominant component of semiaquatic vertebrate faunas. How frogs originated and diversified has long attracted the attention of evolutionary biologists. Here, we recover their evolutionary history by extensive sampling of genes and species and present a hypothesis for frog evolution. In contrast to prior conclusions that the major frog clades were established in the Mesozoic, we find that ∼88% of living frogs originated from three principal lineages that arose at the end of the Mesozoic, coincident with the Cretaceous–Paleogene (K–Pg) mass extinction event that decimated nonavian dinosaurs 66 Mya. The K–Pg extinction events played a pivotal role in shaping the current diversity and geographic distribution of modern frogs.

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Abstract

Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K–Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation.

Fig. 1.

Time-calibrated phylogenetic tree of frogs and the pattern of net diversification rate across time. (A) Evolutionary chronogram based on 95% nuclear genes and 20 fossil age constraints. Gray bars represent the 95% credibility interval of divergence time estimates. Divergence time estimates and corresponding 95% credibility intervals for all nodes are provided in Table S2. Note that the initial diversification of the three major frog clades: Hyloidea (blue), Microhylidae (purple), and Natatanura (green) took place simultaneously near the KPB (dashed red line). (B) Rate-through-time plot of extant frogs indicates an increase in diversification rate at the end of the Cretaceous.

Fig. 2.

Ancestral-area estimates for 69 terminal taxa (families, subfamilies, and genera) of extant frogs using the DEC+J model in BioGeoBEARS. Circles on nodes represent the set of possible ancestral areas, and the color is associated with the area legends. The probabilities are given next to circles for the most probable ancestral area. Circles without values indicate that the probability of the ancestral area is >99%. Three important landmass breakup events are indicated: (A) the break-up of Pangea with division into Laurasia and Gondwana in the Middle Jurassic coincident with the origin of neobatrachian frogs; (B) the separation of Africa and South America in the Early Cretaceous coincident with the divergence of Ranoidea and Hyloidea as well as between the African and New World pipids; and (C) the separation of the Seychelles and India in the Late Cretaceous coincident with the divergence between the Sooglossidae and Nasikabatrachidae. Anuran taxa that contain at least some arboreal species are indicated in green and a tree icon (we do not imply that the last common ancestor of each of these families was arboreal). Note that all clades containing arboreal frogs originated after the KPB.

An promising study suggesting that tooth, dermal scale, epidermal scale, feather and hair evolved in parallel from a shared placode/dermal cells unit, which was present in a common ancestor, an early vertebrate gnathostome, c.a. 420 million years ago

Exp Dermatol. 2017 Jun 11. doi: 10.1111/exd.13391. [Epub ahead of print]

Getting to the root of scales, feather and hair: as deep as odontodes?

Dhouailly D1, Godefroit P2, Martin T3, Nonchev S4, Caraguel F1, Oftedal O5.

Author information

Abstract

While every jawed vertebrate, or its recent ancestor, possesses teeth, skin appendages are characteristic of the living clades: skin denticles (odontodes) in chondrichthyians, dermal scales in teleosts, ducted multicellular glands in amphibians, epidermal scales in squamates, feathers in birds, and hair-gland complexes in mammals, all of them showing a dense periodic patterning. While the odontode origin of teleost scales is generally accepted, the origin of both feather and hair is still debated. They appear long before mammals and birds, at least in Jurassic in mammaliaforms and in ornithodires (pterosaurs and dinosaurs), and are contemporary to scales of early squamates. Epidermal scales might have appeared several times in evolution, and basal amniotes could not have developed a scaled-dry integument, as the function of hair follicle requires its association with glands. In areas such as amnion, cornea or plantar pads, the formation of feather and hair is prevented early in embryogenesis, but can be easily reverted by playing with the Wnt/BMP/Shh pathways, which both imply the plasticity and the default competence of ectoderm. Conserved ectodermal/mesenchymal signaling pathways lead to placode formation, while later the crosstalk differs, as well as the final performing tissue(s): both epidermis and dermis for teeth and odontodes, mostly dermis for teleosts scales, only epidermis for squamate scale, glands, feather and hair. We therefore suggest that tooth, dermal scale, epidermal scale, feather and hair evolved in parallel from a shared placode/dermal cells unit, which was present in a common ancestor, an early vertebrate gnathostome, c.a. 420 million years ago. This article is protected by copyright.

Figure 1. Simplified phylogenetic tree (cladogram) of the major groups of vertebrates. (see supporting information T6 for details and references). A shared and ancestral character is the unit composed of a placode and its associated dermal cells. Such a unit was a key novelty which has been conserved during evolution. It represents the initial step, not only for extant teeth, but also for every type of cutaneous appendage in living vertebrates. Note that fossilized hair, primitive feathers and epidermal scales were found dating back to the Mesozoic era (252-66 mya). In order to simplify the cladogram, a number of clades have been omitted, and the time scale is not accurate. Red bars indicate evolutionary novelty. Note that beta-proteins (formerly beta-keratins) are an evolutionary novelty of sauropsids, while alpha keratins appeared with the first vertebrates.

Those are 2 examples from 100 years ago. Where's the evidence that "frauds are everywhere"?

@willpayton:

I bet you could still find a biology textbook today that has the fraudulent embryo drawings in it.

It was known that they were fraudulent even when they were first created.

Not sure what your point is. I'm sure I can find many things out there. It wouldnt mean anything as far as the general state of the science or of the scientific method or consensus.

@willpayton:

It's important that we talk about these frauds for the very reason you touch on. To keep "science" in a generally good state.

It's absolutely important, but we also cant use isolated cases (from the past) to make categorical judgements on an entire area of study today. If there are examples of frauds being peddled today, as was suggested, I'd like to hear about them. Most of the time when I hear such claims it's just people who are not really familiar with the science and are repeating things they heard online.