Make Your Own Phylogenetic Tree

 
Sandra Porter at Discovering Biology in a Digital World has prepared a short video presentation on how to make your very own phylogenetic tree from DNA sequences [A beginner's guide to making a phylogenetic tree].

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Nisbet Reveals His True Colors

 
Framing is about spin, censorship, and, above all, it's about agreeing with Matt Nisbet and Chris Mooney. If you don't agree with them then it's because you just don't understand framing.

It's about time we started to ignore Nisbet and Mooney. Fortunately, they are making it easy by posting drivel like Why the PZ Myers Affair is Really, Really Bad for Science and PZ Myers, Mind Your Manners (see comments).

I'm opposed to censorship of any kind but I really wish Matt Nisbet and Chris Mooney would voluntarily decide to keep their stupid mouths shut for a few years. I'm with PZ Myers on this one [I'm supposed to sit down and shut up?].

If anyone is really interested in seeing exactly what the blogosphere thinks of Matt Nisbet and Chris Mooney you need only check the links that Greg Laden has posted at The Framing Critique (Dawkins-Myers-Expelled! -Gate). I really hope this spells the beginning of the end for the Nisbet/Mooney tag team.

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Wells Takes a Rain Check on Apology

 
The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.

Evolution News & ViewsI challenged Jonathan Wells to agree to a simple statement that, I believe, might reflect his true beliefs about evolution [A Challenge to Jonathan Wells].

In one of the biggest surprises of the 21st century (not!) Wells has backed off [What’s in a Word?].

Darn. I guess I’ll have to take a rain check on that apology – because I don’t agree with this – and not just because Maurice et al. (2008) are cited incorrectly. Here’s why.

"Evolution" has many meanings. It can mean simply "change over time." The present is different from the past. The cosmos evolves. Technology evolves. No sane person denies evolution in this sense.

Biological evolution never means just change over time, but that's not the real problem with Wells' post. You're going to have to scoot on over to Evolution News & Views and read the whole thing.

I can't make head nor tail of it. I wonder if Wells actually thinks it makes sense?

John Pieret takes on the task of dissecting the Wells definition of evolution on Thoughts in a Haystack [Falling in the Wells]. He's a braver man that I.

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Watch and Weep

 
ABC News follows a group of home-schooled Christian children on a museum tour. The tour leaders are interviewed. They attempt to defend the lies they are telling the children.

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[HatTip: Friendly Atheist: How to Ruin a Trip to the Museuam.]

Evil and Sin

 
Yesterday's issue of the Toronto Star had an article on The fundamentalist atheists.

I'm getting real tired of hearing this phrase but I haven't completely given up trying to understand what people mean when they use it. In this case, the article is by Stuart Laidlaw, who is billed as the "faith and ethics" reporter. Laidlaw is commenting on a recent talk by Chris Hedges. Hedges seems to be one of those "sophisticated" Christians who have all the answers.¹ Naturally, he denigrates the "new atheists" like Richard Dawkins because they just don't understand serious Christianity.

Serious Christians seem to be very concerned about evil and sin.

Hedges, in Toronto recently to promote his book, attacks both fundamentalists and the new breed of atheists as not only intolerant, but wrong about both the Jesus story and the nature of sin.

Sin, he says, is a personal thing that will always be with us. Humans will never outgrow it through evolution, as the atheist authors contend, nor can anyone (Jesus included) relieve us of it, as fundamentalist Christians believe, Hedges says.

The best we can do, he says, is try to mitigate evil by living a good life, and having democratic institutions in place to ensure that we can get rid of bad leaders from time to time.

Sin, as I understand it, is when you violate a moral rule of some kind. It usually means you are disobeying the wishes of supernatural beings. It's not a word used by atheists.

Evil is something I can understand. People do bad things. Religious people do bad things and atheists do bad things. No atheist that I know would ever claim that humans will evolve to the point where they don't do bad things. What a ridiculous idea. What in the world is Hedges thinking?

For fundamentalists, evil and sin are an external force – often represented by Satan – to be vanquished by giving yourself over to Jesus. For the new atheists, evil and sin are the fault of religion, and can be defeated by getting rid of all religion and giving yourself over to scientific, reasoned thought.

For Hedges, it's the same argument: People are basically good, but external forces make us do bad things. Get rid of those forces, and people will be good.

No more effort is needed to achieve utopia, he says.

Just because religions can be evil does not mean that all evil is due to religion. No atheist believes this, as far as I know.

I believe that people are basically good but they still do bad things and they don't need external forces to do them. People are quite capable of being evil all by themselves. What in the world motivates people like Hedges to make up false stories about athiests? It makes him look very silly.

The question of evil and sin seems to be so intertwined with the existence of God that religious people (Christians?) seem to have difficulty untangling them. They seem to think that atheists are as obsessed about evil and sin as they are when, in fact, most of us don't give it much thought. Perhaps that's because we don't have to deal with the paradox of a good God who allows evil and sin?

Hedges draws a distinction between the new breed of atheists and such past non-believers as Albert Camus or scientists of the Enlightenment, whose skepticism he says helped drive human knowledge and understanding.

But Hedges has few such hopes for the new atheists. Where atheists of the past used their disbelief as a stepping off point to find something else to believe in, the new atheists claim to have already found it in what he calls a "cult of science."

Anything that can't be proved scientifically is simply discounted, Hedges says, warning that such a narrow approach to study thwarts the pursuit of knowledge by denying a voice to those who disagree.

The "new atheists" claim there are no supernatural beings because there's no evidence of such beings. This has nothing to do with evil and sin. When are these sophisticated Christians going to address the real question instead of going off on weird tangents? If they have a good argument for the existence of god then let's hear it. Otherwise, their "sophistication" looks more like "obfuscation" to me. (Or like The Emperor's New Clothes and the Courtier's Reply.)

It's time to stop whining and face up to the real question. Is there a god? Questions about evil and sin are irrelevant until that question is settled.

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1. In spite of his confusion about religion, he seems to be a pretty good guy. He was right about Iraq, for example.

The Spin Begins

 
The misreporting of the evolution issue is one key reason for this site. Unfortunately, much of the news coverage has been sloppy, inaccurate, and in some cases, overtly biased. Evolution News & Views presents analysis of that coverage, as well as original reporting that accurately delivers information about the current state of the debate over Darwinian evolution.

Evolution News & ViewsThe Discovery Institute website has skirted around the obvious hypocrisy and attacked Dawkins and Myers. Bruce Chapman has posted an article on Evoluton News & Views about the expulsion of PZ Myers from a viewing of EXPELLED [Richard Dawkins, World’s Most Famous Darwinist, Stoops to Gate-crashing Expelled].

Amazingly, the best selling Oxford scientist/author Richard Dawkins also crashed a showing of Expelled in Minnesota last night and he not only was let in, but introduced at the end of the showing.

Dawkins apparently acknowledged that he had not been invited and did not have a ticket. A sophomoric side to his ideological campaign is thus revealed.

Dawkins, understandably is nervous about this film, among other reasons because Ben Stein has him on camera acknowledging that life on Earth may, indeed, have been intelligently designed, but that it had to have been accomplished by space aliens! This is hilarious, of course, because Dawkins is death on intelligent design. But it turns out that that view applies only if it includes the possibility that the designer might be God.

Myers, of course, relished being expelled from Expelled, but objective observers know that Myers is the most vociferous advocate of expelling Darwin critics from academia. Not from movie pre-screenings where he wasn’t invited, mind you, but from their jobs. Too bad the film doesn’t show (and I wish it had), his promotion of advice to attack teachers and professors who dare question Darwin’s theory. The whole point of Myers is that he is a take-no-prisoners, crusading atheist scientist who has made it his purpose in life to harass people who disagree with him. Dawkins turns out to be his buddy and mutual admirer.

Those of you who have been following the issue on the various blogs, and in newspaper articles, know full well that Dawkins did not "crash" the movie. People did not have to be invited and there were no tickets. Chapman and his friends must know this too. Therefore, he is lying.

I'm not surprised that most of the IDiots are behaving this way. What will surprise me is that all of them might behave like Bruce Chapman. I expect at least one prominent IDiot to admit that expelling PZ Myers was a mistake and to admit that he should have been allowed to see a movie that featured him.

Let's see if there's at least one IDiot with the guts to speak the truth. Bill Dembski is not going to be that person (suprise!) because he has just posted the Chapman piece on his blog [Discovery News Release on Richard Dawkins Crashing EXPELLED Screening]. I'm hoping that Denyse O'Leary will be the one with the gumption. Or maybe Michael Behe. I expect Jonathan Wells to weigh in with even more lies about the incident.

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PZ Myers and Richard Dawkins Discuss "EXPELLED"

 
New York Times article by Cornelia Dean: No Admission for Evolutionary Biologist at Creationist Film.

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[HatTip: RichardDawkins.net]

EXPELLED! - Waiting for the Creationists to repsond ...

 
By now you've all heard the news. PZ Myers was standing in line to see a screening of the propaganda movie EXPELLED when security guards asked him to leave. They didn't bother with his family or his friend, Richard Dawkins. Read PZ's account at EXPELLED!.

Now let's see how the creationists respond to this incident. Remember, the movie is about discrimination by scientists against people who are religious. It will be very interesting to see how they can justify keeping PZ Myers out of the movie when all kinds of other people were let in.

Here's one response, posted on the EXPELLED website [Richard Dawkins crashes the party at a screening of “Expelled”]. The writer is Stuart Blessman, a Christian who was given tickets to see the movie by his pastor. Blessman was present at the theater on Wednesday evening. He is responding to the charge that PZ Myers was prevented from seeing the movie because he (PZ) is an evolutionist. Here's what Stuart Blessman says ...

I just happened to be standing directly in line behind Dawkins’ academic colleague. Management of the movie theatre saw a man apparently hustling and bothering several invited attendees, apparently trying to disrupt the viewing or sneak in. Management then approached the man, asked him if he had a ticket, and when he confirmed that he didn’t, they then escorted him off the premises. Nowhere was one of the film’s producers to be found, and the man certainly didn’t identify himself. If a producer had been nearby, it’s possible that he would have been admitted, but the theatre’s management didn’t want to take any chances.

This sounds very much like a blatant, bare-faced, lie. Anyone who knows PZ Myers would know that he would bot be "hustling" and "bothering" the people waiting in line. Quite the contrary, PZ and his colleague Richard Dawkins would have been trying to keep a low profile.

In his followup posting, PZ responds by saying that Blessman's account is a complete fabrication [A late night quick one].

Now, I'm going to be looking in on creationist blogs to see how they handle this story. So far there has been deathly silence. Is that because the creationists are embarrassed? Is it because they never criticize their own kind? Or, is it because they don't see the hypocrisy? Please let me know of any creationist responses.

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Communicating Science in a Religious America

 
"Communicating Science in a Religous America" was the title of a session at the AAAS meeting in February. Here's a summary of the meeting from someone who seems to have been paying attention [Puttin Science in a Frame]. Here's a teaser ...

Framing has not been without controversy, as some have viewed it as little more than a form of empty platitude or an attempt to dumb down science. What became clear from Nisbet's talk, however, is that there can also be people left out of the ostensibly-shared values; it should be no surprise they are objecting.

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Going Public with the Scientific Process

 
Ruth Cronje is a faculty member of the Scientific and Technical Writing Program at the University of Wisconsin-Eau Claire in Eau Claire, WI (USA). She has written a letter that was published in Science last week [Going Public with the Scientific Process]. Many of you will never get to read it but you should. It is wonderful.

I'm going to take a chance here and publish her entire letter just so it gets as wide a coverage as possible.

The idea of using framing strategies to communicate science to the public has recently been taken up in scientific forums (1, 2), the mainstream media (3), and the blogosphere (4, 5). Most participants in the framing science debate limit their notion of scientific information to scientific facts. However, confining science messages to just the facts interferes with public understanding of science as a systematic, logical process of human inquiry and effaces the distinction between data and scientists' reasoning about data. To communicate successfully, we should focus on scientific process by emphasizing two important elements of scientific rationality: skepticism and dynamicism (6, 7).

Scientists deliberately integrate skepticism into their procedures by trying to refute their own hypotheses, retaining them only when confronted with compelling evidence sought through carefully controlled procedures. Scientists tend to shy away from revealing the intrinsic skepticism of science to the public, fearful that it will open the door to doubt about the validity of their conclusions. But communicating only the facts of science (framed or unframed) destabilizes public confidence in science. A fact doesn't allow science communicators to reveal, justify, and ultimately promote the skeptical reasoning process that helps make scientists more confident that their reasoning is correct.

Science is also dynamic; it is a cumulative enterprise that requires scientists to situate their instrumental activities and interpretations against the evidence that has come before and to alter them in light of new evidence. Insisting that new data be interpreted within the context of past and future data will ferret out and correct error over time, but it means that a fact cannot, by definition, be anything more than the (ephemeral and fallible) consensus of scientists at a given point in time. A "just the facts" strategy can and often does backfire, ultimately fueling public alienation from science. When scientists inform the public of "facts" (like the "fact" widely disseminated in the 1970s that all dietary fats are bad for us), and then that "fact" is refined or altered (now we're told olive oil is good for us), the public is justifiably confused. Studies suggest that the public tends to regard normal scientific refinement and self-correction as equivocation or incompetence (8-10). Instead of sweeping uncertainty under the rug, science communicators should help the public understand the logical and systematic procedures by which scientists confront it.

The true majesty and promise of science lies in its systematic, logical, skeptical, and dynamic reasoning procedures. "Successful" science communication should not be regarded as any message that enlists public support for science. Rather, we should define "success" in scientific communication as achieving a public that celebrates scientific reasoning procedures.

In case Mathews and Nisbet don't get it, the new version of Science journal isn't going to let them get away with distorting science for political ends. Nisbet comments on this letter and hopes to discuss the topic with Cronje when he visits her next week [At Science, Still More Reaction to Framing]. I'd love to be there.

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Bruce Alberts on Science Education

 
Bruce Alberts, the former President of the National Academies (USA), has now taken over as Editor-in-Chief of Science.¹ Judging by his editorial in this week's issue [Considering Science Education] there could be some interesting times ahead in the Science offices.

Here's part of what Bruce has to say about science education ...

I consider science education to be critically important to both science and the world, and I shall frequently address this topic on this page. Let’s start with a big-picture view. The scientific enterprise has greatly advanced our understanding of the natural world and has thereby enabled the creation of countless medicines and useful devices. It has also led to behaviors that have improved lives. The public appreciates these practical benefits of science, and science and scientists are generally respected, even by those who are not familiar with how science works or what exactly it has discovered.

But society may less appreciate the advantage of having everyone aquire, as part of their formal education, the ways of thinking and behaving that are central to the practice of successful science: scientific habits of mind. These habits include a skeptical attitude toward dogmatic claims and a strong desire for logic and evidence. As famed astronomer Carl Sagan put it, science is our best “bunk” detector. Individuals and societies clearly need a means to logically test the onslaught of constant clever attempts to manipulate our purchasing and political decisions. They also need to challenge what is irrational, including the intolerance that fuels so many regional and global conflicts.

So how does this relate to science education? Might it be possible to encourage, across the world, scientific habits of mind, so as to create more rational societies everywhere? In principle, a vigorous expansion of science education could provide the world with such an opportunity, but only if scientists, educators, and policy-makers redefine the goals of science education, beginning with college-level teaching. Rather than only conveying what science has discovered about the natural world, as is done now in most countries, a top priority should be to empower all students with the knowledge and practice of how to think like a scientist.

Those of you who have been reading Sandwalk know that this is exactly how I think science education should be fixed. We need to teach students how to think like a scientist. The facts of science are important but they aren't nearly as important as the way in which scientific facts are determined. Science is a way of knowing—that's what students need to learn.

I think we have a long way to go. At SciBarCamp last weekend we discussed the ten things everyone needs to know about science. One of the things on my original list was that science is a way of knowing [Ten Things Everyone Should Know About Science]. Before the meeting someone had written a comment on the poster to the effect that science may not be the only way of knowing and another participate wrote in that "it kinda was."

When it came time for the discussion the moderator handed out three topics to each of the panel members. One of them got the topic "Science doesn't have all the answers" and I was given the topic "Science has all the answers." When it came time for me to present I said that science doesn't have all the answers and nobody I know claims otherwise.

I changed the topic to "science is a way of knowing" and suggested that it may be the only way of knowing. Considerable debate followed. It was clear that many participants were new to this topic since the old arguments about love and morality came up.

At the end of the session, the moderator wrapped up and concluded that there was consensus on three things everyone needs to know about science. One of them was "science doesn't have all the answers." This is completely wrong, in my opinion. Of course, science doesn't have all the answers. The real question is whether it has all the questions.

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1. In the interests of full disclosure, I should reveal that he was also my graduate supervisor. (See Bruce Alberts in Toronto.)

Tangled Bank #101

 
The latest issue of Tangled Bank is #101. It's hosted at Tangled Up in Blue Guy [Tangled Bank #101].

When I first found that I would be hosting this edition of Tangled Bank, I tried to come up with a theme centered on Highway 101. It runs along the West Coast in the US and A and a stretch of it through San Francisco is also known as Van Ness Boulevard. I lived a block away from Van Ness for a year and one of my favorite pubs was an English Local, known as Highway 101. The idea for a clever theme vanished when I started receiving and reading the submissions that people sent. I decided I didn’t want to detract from the entries featured by making the show gimmicky. The Tangled Bank isn’t about me, it’s about science and the excitement of discovery as people unravel the mysteries of the natural world.

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

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Fun in Guelph

 
Katie Kish has a brief description of my visit to Guelph on her blog Liberal Debutante [Larry Moran At Guelph. I stole the photograph from her, I hope she doesn't mind.

The question about the evolution of the bombardier beetle was really a question about irreducible complexity in general and I tried to answer that question rather than the specific question that was asked. I was pretty sure that Dawkins had refuted the bombardier beetle "paradox" with real examples of transitional forms but I wasn't sure about this and didn't know the reference. (I said at the talk that I thought it was in The Blind Watchmaker).

Ryan Gregory, who I met for the first time on Wednesday night, has come to the rescue with a posting on Genomicron [Bombardier Beetles]. He has even found a video of Richard Dawkins "exploding" the myth of exploding bombardier beetles. Go and watch it on Ryan's blog.

There's an important lesson here. It is 2008. The evolutionary "problem" represented by the bombardier beetle was addressed—and refuted—by evolutionary biologists over 20 years ago and yet it's still being raised today by creationists as if it were a serious problem. What does that tell you about creationists?

Dealing with IDiots is very frustrating.

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Nobel Laureate: Paul Flory

 

The Nobel Prize in Chemistry 1974.

"for his fundamental achievements, both theoretical and experimental, in the physical chemistry of the macromolecules"


In 1974, Paul J. Flory (1910 - 1985) was awarded the Nobel Prize in Chemistry for his work on the physical chemistry of macromolecules in solution. His work led to an understanding of the dynamics and conformation of proteins and that's why his contributions are covered in biochemistry courses.

The presentation speech was delivered by Professor Stig Claesson of the Royal Academy of Sciences.THEME:

Nobel Laureates

Your Majesty, Your Royal Highnesses, Ladies and Gentlemen,

This year's Nobel prize in chemistry has been awarded to Professor Paul Flory for his fundamental contributions to the physical chemistry of macromolecules.

Macromolecules include biologically important materials such as cellulose, albumins and nucleic acids, and all of our plastics and synthetic fibers.

Macromolecules are often referred to as chain molecules and can be compared to a pearl necklace. They consist of long chains of atoms which, when magnified one hundred million times, appear as a pearl necklace. The pearls represent the atoms in the chain. One should realize that this chain is much longer than the necklaces being worn here this evening. To obtain a representative model of a macromolecule all of the necklaces here in this hall should be connected together in a single long chain.

One can readily appreciate that the development of a theory for these molecules presented considerable difficulties. The forms of the chain itself, whether extended or coiled, represents a property difficult to rationalize.

A statistical description is of necessity required, and Professor Flory has made major contributions to the development of such a theory. The problem is more difficult, however. How can one compare different molecules in different solvents?

When chain molecules are dissolved in different solvents they become coiled to different degrees, depending on the interaction between repulsive and attractive forces in the solution. In a good solvent the chain molecules are extended. In a poor solvent, in contrast, the chain molecules assume a highly coiled form.

Professor Flory showed that if one takes a solution of extended chain molecules in a good solvent, and slowly cools the solution, then the molecules become progressively more coiled until they are no longer soluble.

Thus, there must be an intermediate temperature where the attractive and repulsive forces are balanced. At this temperature the molecules assume a kind of standard condition that can be used, generally, to characterize their properties.

This temperature Professor Flory named the theta temperature. A corresponding temperature exists for real gases at which they follow the ideal gas law. This temperature is called the Boyle temperature after Robert Boyle who discovered the gas laws. By analogy, the theta temperature for macromolecules is often referred to as the Flory temperature.

Profssor Flory showed also that it was possible to define a constant for chain molecules, now called Flory's universal constant, which can be compared in significance to the gas constant.

When one, in retrospect, reads about an important scientific discovery, one often feels that the work was remarkably simple. This actually indicates, however, that it was brilliant insight in a new and until then unexplored research area. This is highly characteristic of Professor Flory's scientific discoveries, not only those concerned with the Flory temperature and Flory's universal constant but also many of his other important research studies. Further examples are found in his investigation of the relationship between the reaction mechanism and the length of the chains formed when chain molecules are prepared synthetically, as well as his important contribution to the theory of crystallization and rubber elasticity. These achievements have been of major importance for technological developments in the plastics industry.

In recent years Professor Flory has investigated, both theoretically and experimentally, the relation between rotational characteristics of the chain links and the form of the chain molecules. This is of fundamental significance for the understanding of both biological macromolecules and synthetic chain molecules.

During the time Professor Flory has been active as a scientist, macromolecular chemistry has been transformed from primitive semi-empirical observations into a highly developed science. This evolution has come about through major contributions by research groups from both universities and many of the world's largest industrial laboratories. Professor Flory has remained a leading researcher in the area during this entire period, giving further evidence of his unique position as a scientist.

Professor Flory,

I have tried to describe briefly the fundamental importance of your many contributions to macromolecular chemistry and in particular those concepts introduced by you and now referred to as the Flory-temperature and the Flory universal constant.

On behalf of the Royal Academy of Sciences I wish to convey to you our warmest congratulations and I now ask you to receive your prize from the hands of His Majesty the King.

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Gene Genie #27

 
The 27th edition of Gene Genie has been posted at DNA Direct Talk [The Gene Genie: Yes, But What About Me?].

Welcome to another edition of Gene Genie, the blog carnival about genes, genomics and gene-related diseases. With Craig Venter and 23andMe and decodeME all over the news, I thought this edition might be appropriately focused on genes and “me.” What does the gene genie have to say about us?

The beautiful logo was created by Ricardo at My Biotech Life.

The purpose of this carnival is to highlight the genetics of one particular species, Homo sapiens.

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