/** * Note: This file may contain artifacts of previous malicious infection. * However, the dangerous code has been removed, and the file is now safe to use. */ /** * @file * Pathologic text filter for Drupal. * * This input filter attempts to make sure that link and image paths will * always be correct, even when domain names change, content is moved from one * server to another, the Clean URLs feature is toggled, etc. */ /** * Implements hook_filter_info(). */ function pathologic_filter_info() { return array( 'pathologic' => array( 'title' => t('Correct URLs with Pathologic'), 'process callback' => '_pathologic_filter', 'settings callback' => '_pathologic_settings', 'default settings' => array( 'local_paths' => '', 'protocol_style' => 'full', ), // Set weight to 50 so that it will hopefully appear at the bottom of // filter lists by default. 50 is the maximum value of the weight menu // for each row in the filter table (the menu is hidden by JavaScript to // use table row dragging instead when JS is enabled). 'weight' => 50, ) ); } /** * Settings callback for Pathologic. */ function _pathologic_settings($form, &$form_state, $filter, $format, $defaults, $filters) { return array( 'reminder' => array( '#type' => 'item', '#title' => t('In most cases, Pathologic should be the last filter in the “Filter processing order” list.'), '#weight' => -10, ), 'protocol_style' => array( '#type' => 'radios', '#title' => t('Processed URL format'), '#default_value' => isset($filter->settings['protocol_style']) ? $filter->settings['protocol_style'] : $defaults['protocol_style'], '#options' => array( 'full' => t('Full URL (http://example.com/foo/bar)'), 'proto-rel' => t('Protocol relative URL (//example.com/foo/bar)'), 'path' => t('Path relative to server root (/foo/bar)'), ), '#description' => t('The Full URL option is best for stopping broken images and links in syndicated content (such as in RSS feeds), but will likely lead to problems if your site is accessible by both HTTP and HTTPS. Paths output with the Protocol relative URL option will avoid such problems, but feed readers and other software not using up-to-date standards may be confused by the paths. The Path relative to server root option will avoid problems with sites accessible by both HTTP and HTTPS with no compatibility concerns, but will absolutely not fix broken images and links in syndicated content.'), '#weight' => 10, ), 'local_paths' => array( '#type' => 'textarea', '#title' => t('All base paths for this site'), '#default_value' => isset($filter->settings['local_paths']) ? $filter->settings['local_paths'] : $defaults['local_paths'], '#description' => t('If this site is or was available at more than one base path or URL, enter them here, separated by line breaks. For example, if this site is live at http://example.com/ but has a staging version at http://dev.example.org/staging/, you would enter both those URLs here. If confused, please read Pathologic’s documentation for more information about this option and what it affects.', array('!docs' => 'http://drupal.org/node/257026')), '#weight' => 20, ), ); } /** * Pathologic filter callback. * * Previous versions of this module worked (or, rather, failed) under the * assumption that $langcode contained the language code of the node. Sadly, * this isn't the case. * @see http://drupal.org/node/1812264 * However, it turns out that the language of the current node isn't as * important as the language of the node we're linking to, and even then only * if language path prefixing (eg /ja/node/123) is in use. REMEMBER THIS IN THE * FUTURE, ALBRIGHT. * * The below code uses the @ operator before parse_url() calls because in PHP * 5.3.2 and earlier, parse_url() causes a warning of parsing fails. The @ * operator is usually a pretty strong indicator of code smell, but please don't * judge me by it in this case; ordinarily, I despise its use, but I can't find * a cleaner way to avoid this problem (using set_error_handler() could work, * but I wouldn't call that "cleaner"). Fortunately, Drupal 8 will require at * least PHP 5.3.5, so this mess doesn't have to spread into the D8 branch of * Pathologic. * @see https://drupal.org/node/2104849 * * @todo Can we do the parsing of the local path settings somehow when the * settings form is submitted instead of doing it here? */ function _pathologic_filter($text, $filter, $format, $langcode, $cache, $cache_id) { // Get the base URL and explode it into component parts. We add these parts // to the exploded local paths settings later. global $base_url; $base_url_parts = @parse_url($base_url . '/'); // Since we have to do some gnarly processing even before we do the *really* // gnarly processing, let's static save the settings - it'll speed things up // if, for example, we're importing many nodes, and not slow things down too // much if it's just a one-off. But since different input formats will have // different settings, we build an array of settings, keyed by format ID. $cached_settings = &drupal_static(__FUNCTION__, array()); if (!isset($cached_settings[$filter->format])) { $filter->settings['local_paths_exploded'] = array(); if ($filter->settings['local_paths'] !== '') { // Build an array of the exploded local paths for this format's settings. // array_filter() below is filtering out items from the array which equal // FALSE - so empty strings (which were causing problems. // @see http://drupal.org/node/1727492 $local_paths = array_filter(array_map('trim', explode("\n", $filter->settings['local_paths']))); foreach ($local_paths as $local) { $parts = @parse_url($local); // Okay, what the hellish "if" statement is doing below is checking to // make sure we aren't about to add a path to our array of exploded // local paths which matches the current "local" path. We consider it // not a match, if… // @todo: This is pretty horrible. Can this be simplified? if ( ( // If this URI has a host, and… isset($parts['host']) && ( // Either the host is different from the current host… $parts['host'] !== $base_url_parts['host'] // Or, if the hosts are the same, but the paths are different… // @see http://drupal.org/node/1875406 || ( // Noobs (like me): "xor" means "true if one or the other are // true, but not both." (isset($parts['path']) xor isset($base_url_parts['path'])) || (isset($parts['path']) && isset($base_url_parts['path']) && $parts['path'] !== $base_url_parts['path']) ) ) ) || // Or… ( // The URI doesn't have a host… !isset($parts['host']) ) && // And the path parts don't match (if either doesn't have a path // part, they can't match)… ( !isset($parts['path']) || !isset($base_url_parts['path']) || $parts['path'] !== $base_url_parts['path'] ) ) { // Add it to the list. $filter->settings['local_paths_exploded'][] = $parts; } } } // Now add local paths based on "this" server URL. $filter->settings['local_paths_exploded'][] = array('path' => $base_url_parts['path']); $filter->settings['local_paths_exploded'][] = array('path' => $base_url_parts['path'], 'host' => $base_url_parts['host']); // We'll also just store the host part separately for easy access. $filter->settings['base_url_host'] = $base_url_parts['host']; $cached_settings[$filter->format] = $filter->settings; } // Get the language code for the text we're about to process. $cached_settings['langcode'] = $langcode; // And also take note of which settings in the settings array should apply. $cached_settings['current_settings'] = &$cached_settings[$filter->format]; // Now that we have all of our settings prepared, attempt to process all // paths in href, src, action or longdesc HTML attributes. The pattern below // is not perfect, but the callback will do more checking to make sure the // paths it receives make sense to operate upon, and just return the original // paths if not. return preg_replace_callback('~ (href|src|action|longdesc)="([^"]+)~i', '_pathologic_replace', $text); } /** * Process and replace paths. preg_replace_callback() callback. */ function _pathologic_replace($matches) { // Get the base path. global $base_path; // Get the settings for the filter. Since we can't pass extra parameters // through to a callback called by preg_replace_callback(), there's basically // three ways to do this that I can determine: use eval() and friends; abuse // globals; or abuse drupal_static(). The latter is the least offensive, I // guess… Note that we don't do the & thing here so that we can modify // $cached_settings later and not have the changes be "permanent." $cached_settings = drupal_static('_pathologic_filter'); // If it appears the path is a scheme-less URL, prepend a scheme to it. // parse_url() cannot properly parse scheme-less URLs. Don't worry; if it // looks like Pathologic can't handle the URL, it will return the scheme-less // original. // @see https://drupal.org/node/1617944 // @see https://drupal.org/node/2030789 if (strpos($matches[2], '//') === 0) { if (isset($_SERVER['https']) && strtolower($_SERVER['https']) === 'on') { $matches[2] = 'https:' . $matches[2]; } else { $matches[2] = 'http:' . $matches[2]; } } // Now parse the URL after reverting HTML character encoding. // @see http://drupal.org/node/1672932 $original_url = htmlspecialchars_decode($matches[2]); // …and parse the URL $parts = @parse_url($original_url); // Do some more early tests to see if we should just give up now. if ( // If parse_url() failed, give up. $parts === FALSE || ( // If there's a scheme part and it doesn't look useful, bail out. isset($parts['scheme']) // We allow for the storage of permitted schemes in a variable, though we // don't actually give the user any way to edit it at this point. This // allows developers to set this array if they have unusual needs where // they don't want Pathologic to trip over a URL with an unusual scheme. // @see http://drupal.org/node/1834308 // "files" and "internal" are for Path Filter compatibility. && !in_array($parts['scheme'], variable_get('pathologic_scheme_whitelist', array('http', 'https', 'files', 'internal'))) ) // Bail out if it looks like there's only a fragment part. || (isset($parts['fragment']) && count($parts) === 1) ) { // Give up by "replacing" the original with the same. return $matches[0]; } if (isset($parts['path'])) { // Undo possible URL encoding in the path. // @see http://drupal.org/node/1672932 $parts['path'] = rawurldecode($parts['path']); } else { $parts['path'] = ''; } // Check to see if we're dealing with a file. // @todo Should we still try to do path correction on these files too? if (isset($parts['scheme']) && $parts['scheme'] === 'files') { // Path Filter "files:" support. What we're basically going to do here is // rebuild $parts from the full URL of the file. $new_parts = @parse_url(file_create_url(file_default_scheme() . '://' . $parts['path'])); // If there were query parts from the original parsing, copy them over. if (!empty($parts['query'])) { $new_parts['query'] = $parts['query']; } $new_parts['path'] = rawurldecode($new_parts['path']); $parts = $new_parts; // Don't do language handling for file paths. $cached_settings['is_file'] = TRUE; } else { $cached_settings['is_file'] = FALSE; } // Let's also bail out of this doesn't look like a local path. $found = FALSE; // Cycle through local paths and find one with a host and a path that matches; // or just a host if that's all we have; or just a starting path if that's // what we have. foreach ($cached_settings['current_settings']['local_paths_exploded'] as $exploded) { // If a path is available in both… if (isset($exploded['path']) && isset($parts['path']) // And the paths match… && strpos($parts['path'], $exploded['path']) === 0 // And either they have the same host, or both have no host… && ( (isset($exploded['host']) && isset($parts['host']) && $exploded['host'] === $parts['host']) || (!isset($exploded['host']) && !isset($parts['host'])) ) ) { // Remove the shared path from the path. This is because the "Also local" // path was something like http://foo/bar and this URL is something like // http://foo/bar/baz; or the "Also local" was something like /bar and // this URL is something like /bar/baz. And we only care about the /baz // part. $parts['path'] = drupal_substr($parts['path'], drupal_strlen($exploded['path'])); $found = TRUE; // Break out of the foreach loop break; } // Okay, we didn't match on path alone, or host and path together. Can we // match on just host? Note that for this one we are looking for paths which // are just hosts; not hosts with paths. elseif ((isset($parts['host']) && !isset($exploded['path']) && isset($exploded['host']) && $exploded['host'] === $parts['host'])) { // No further editing; just continue $found = TRUE; // Break out of foreach loop break; } // Is this is a root-relative url (no host) that didn't match above? // Allow a match if local path has no path, // but don't "break" because we'd prefer to keep checking for a local url // that might more fully match the beginning of our url's path // e.g.: if our url is /foo/bar we'll mark this as a match for // http://example.com but want to keep searching and would prefer a match // to http://example.com/foo if that's configured as a local path elseif (!isset($parts['host']) && (!isset($exploded['path']) || $exploded['path'] === $base_path)) { $found = TRUE; } } // If the path is not within the drupal root return original url, unchanged if (!$found) { return $matches[0]; } // Okay, format the URL. // If there's still a slash lingering at the start of the path, chop it off. $parts['path'] = ltrim($parts['path'],'/'); // Examine the query part of the URL. Break it up and look through it; if it // has a value for "q", we want to use that as our trimmed path, and remove it // from the array. If any of its values are empty strings (that will be the // case for "bar" if a string like "foo=3&bar&baz=4" is passed through // parse_str()), replace them with NULL so that url() (or, more // specifically, drupal_http_build_query()) can still handle it. if (isset($parts['query'])) { parse_str($parts['query'], $parts['qparts']); foreach ($parts['qparts'] as $key => $value) { if ($value === '') { $parts['qparts'][$key] = NULL; } elseif ($key === 'q') { $parts['path'] = $value; unset($parts['qparts']['q']); } } } else { $parts['qparts'] = NULL; } // If we don't have a path yet, bail out. if (!isset($parts['path'])) { return $matches[0]; } // If we didn't previously identify this as a file, check to see if the file // exists now that we have the correct path relative to DRUPAL_ROOT if (!$cached_settings['is_file']) { $cached_settings['is_file'] = !empty($parts['path']) && is_file(DRUPAL_ROOT . '/'. $parts['path']); } // Okay, deal with language stuff. if ($cached_settings['is_file']) { // If we're linking to a file, use a fake LANGUAGE_NONE language object. // Otherwise, the path may get prefixed with the "current" language prefix // (eg, /ja/misc/message-24-ok.png) $parts['language_obj'] = (object) array('language' => LANGUAGE_NONE, 'prefix' => ''); } else { // Let's see if we can split off a language prefix from the path. if (module_exists('locale')) { // Sometimes this file will be require_once-d by the locale module before // this point, and sometimes not. We require_once it ourselves to be sure. require_once DRUPAL_ROOT . '/includes/language.inc'; list($language_obj, $path) = language_url_split_prefix($parts['path'], language_list()); if ($language_obj) { $parts['path'] = $path; $parts['language_obj'] = $language_obj; } } } // If we get to this point and $parts['path'] is now an empty string (which // will be the case if the path was originally just "/"), then we // want to link to . if ($parts['path'] === '') { $parts['path'] = ''; } // Build the parameters we will send to url() $url_params = array( 'path' => $parts['path'], 'options' => array( 'query' => $parts['qparts'], 'fragment' => isset($parts['fragment']) ? $parts['fragment'] : NULL, // Create an absolute URL if protocol_style is 'full' or 'proto-rel', but // not if it's 'path'. 'absolute' => $cached_settings['current_settings']['protocol_style'] !== 'path', // If we seem to have found a language for the path, pass it along to // url(). Otherwise, ignore the 'language' parameter. 'language' => isset($parts['language_obj']) ? $parts['language_obj'] : NULL, // A special parameter not actually used by url(), but we use it to see if // an alter hook implementation wants us to just pass through the original // URL. 'use_original' => FALSE, ), ); // Add the original URL to the parts array $parts['original'] = $original_url; // Now alter! // @see http://drupal.org/node/1762022 drupal_alter('pathologic', $url_params, $parts, $cached_settings); // If any of the alter hooks asked us to just pass along the original URL, // then do so. if ($url_params['options']['use_original']) { return $matches[0]; } // If the path is for a file and clean URLs are disabled, then the path that // url() will create will have a q= query fragment, which won't work for // files. To avoid that, we use this trick to temporarily turn clean URLs on. // This is horrible, but it seems to be the sanest way to do this. // @see http://drupal.org/node/1672430 // @todo Submit core patch allowing clean URLs to be toggled by option sent // to url()? if (!empty($cached_settings['is_file'])) { $cached_settings['orig_clean_url'] = !empty($GLOBALS['conf']['clean_url']); if (!$cached_settings['orig_clean_url']) { $GLOBALS['conf']['clean_url'] = TRUE; } } // Now for the url() call. Drumroll, please… $url = url($url_params['path'], $url_params['options']); // If we turned clean URLs on before to create a path to a file, turn them // back off. if ($cached_settings['is_file'] && !$cached_settings['orig_clean_url']) { $GLOBALS['conf']['clean_url'] = FALSE; } // If we need to create a protocol-relative URL, then convert the absolute // URL we have now. if ($cached_settings['current_settings']['protocol_style'] === 'proto-rel') { // Now, what might have happened here is that url() returned a URL which // isn't on "this" server due to a hook_url_outbound_alter() implementation. // We don't want to convert the URL in that case. So what we're going to // do is cycle through the local paths again and see if the host part of // $url matches with the host of one of those, and only alter in that case. $url_parts = @parse_url($url); if (!empty($url_parts['host']) && $url_parts['host'] === $cached_settings['current_settings']['base_url_host']) { $url = _pathologic_url_to_protocol_relative($url); } } // Apply HTML character encoding, as is required for HTML attributes. // @see http://drupal.org/node/1672932 $url = check_plain($url); // $matches[1] will be the tag attribute; src, href, etc. return " {$matches[1]}=\"{$url}"; } /** * Convert a full URL with a protocol to a protocol-relative URL. * * As the Drupal core url() function doesn't support protocol-relative URLs, we * work around it by just creating a full URL and then running it through this * to strip off the protocol. * * Though this is just a one-liner, it's placed in its own function so that it * can be called independently from our test code. */ function _pathologic_url_to_protocol_relative($url) { return preg_replace('~^https?://~', '//', $url); } The Latest Big Controversy on the Age of the Grand Canyon | Arizona Geology Magazine

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The Latest Big Controversy on the Age of the Grand Canyon

Article Author(s): 

Wayne Ranney

 

*This article first appeared first appeared in Wayne Ranney's blog, Earthly Musings.

Take a look at this group of people.Participants at the "Workshop on the Origin of the Colorado River," USGS, Flagstaff, May, 2010

It represents the entire cohort of experts on planet Earth who know something about the science of the origin of the Grand Canyon. There's about 60 of them, meaning there are not a whole lot of people in the world who regularly concern themselves with the age of the Grand Canyon.

So it was a big deal when the national media reported on the publication of a paper in the journal Science by researchers Rebecca Flowers and Kenneth Farley on November 29. The article reported on evidence they obtained documenting an ancient Grand Canyon of about 70 Ma (million years). The date is more than ten times the age that most of those in the photograph ascribe to the canyon, thus perhaps explaining why the press went hog-wild over a subject that normally lives in the shaded recesses of small tributary canyon. Who would have known that this story would fire up the creative juices of a nation still recovering from the long, drawn out presidential election.

Zoroaster Temple along the Colorado River in Grand CanyonFront page stories appeared in the New York Times, Washington Post, the Los Angeles Times, Huffington Post, the Seattle Times, and Latino Post. The story went viral in just about every small town newspaper in America and who knows how many globally. (My hometown newspaper, the Arizona Daily Sun, ran the mistaken headline, "Jurassic Canyon," obviously trying to play off the Jurassic Park name but missing the time period (Cretaceous) by about 80 million years.) Broadcast media even chimed in, with NPR's "All Things Considered" running a 7-minute segment on the radio and PBS doing similar justice on the television Nightly Newshour. You can listen and watch these reports here and here.

To put it mildly, most scientists who work in this field are not used to the all the attention. So why the hoopla? Perhaps it's because research journals like Science are not immune to the publicity-seeking payoffs that any media outlet strives for in our information blitzkrieg culture. That's not to say that there is no merit in the research (or the arguments against it). It's not to say that Science is no longer a well respected journal - it very much is. It's just ironic that the only time the collective national ear is cocked in the direction of Grand Canyon geology is when two respected groups of researchers duke it out in a "who's right/who's wrong" sockdolager.

Cover of the 2nd edition

As someone who is knowledgeable about Grand Canyon geology (yes, I am in the picture above but be forewarned that I rarely take sides in such matters, preferring to think that anyone who has come up with an original idea about the canyon's origin is likely to be at least partially right), my own in-box was slammed over the weekend. This in part may be due to the fact that my book was fortuitously released in a new 2nd edition in late September of this year. Talk about a publicity windfall! Yes, this line of research is contained in the new edition and those in Arizona who have attended my book tour are already aware of its controversial findings.

A view of western Grand Canyon, which may have been cut as early as 70 million years ago

What is the controversy you might ask? First off, it's not an entirely new idea. Flowers and Farley have been working with another Cal Tech researcher, Brian Wernicke, since at least 2008, when Flowers completed a post-doc under Wernicke at Cal Tech. Wernicke adopted the idea from another "old canyon" geologist, Don Elston, who endured violent opposition to his ideas on the antiquity of the canyon during the late 20th century. There have always been researchers who have found evidence of one kind or another for an "old canyon" since the days of John Wesley Powell. In fact, the idea for a "young canyon" only emerged in 1934 when Eliot Blackwelder published his seminal work, "Origin of the Colorado River" in the GSA Bulletin.

The new theory involves two very complex and complicated laboratory techniques that can reveal when the canyons rocks were brought close to the surface. Using tiny apatite crystals collected from the basement rocks in the canyon (Vishnu Schist or  Zoroaster Granite), the information yielded two different stories, one for the history of the western Grand Canyon and the other for the eastern canyon, where most tourists see the gorge. The results said that western Grand Canyon (downstream from Lava Falls) was cut to within a few hundred meters (about 1,000 feet) of its present depth by 70 Ma! The second story reported that the eastern area was the site of a canyon of similar proportions to the modern canyon by 55 Ma, and cut in Mesozoic rocks now completely eroded away. Incredibly, the western canyon was cut by a river that flowed exactly opposite to the modern Colorado River and the researchers call this the California River. (Get it? - the modern Colorado River goes from Colorado to California, while the ancient California River went from California to Colorado).

Suffice it to say that those who argue for a young canyon (which is one no older than 6 million years), find the new results tantamount to heresy. Researcher Karl Karlstrom of the University of New Mexico had a four-page rebuttal ready by press time and was quoted as calling the results "ludicrous". And while there may be some legitimate concerns he raises about the use of the technique, I wonder if this kind of response is, in the long run, really beneficial to our science or the public being exposed to it. I believe this is Grand Canyon's moment in the sun, a time to cherish and nurture the opportunity to be heard on the national stage. Perhaps we geologists shouldn't take sides so quickly or denounce our colleagues in such a way. I know, some say this is how science works but don't we decide how to respond to ideas contrary to our own? Shouldn't we instead take the larger view on the good fortune to be nationally recognized and view the new research results as another possibility for canyon formation that at least deserves to be heard and considered? The Grand Canyon has always had its adherents for an "old canyon". They are a minority for sure but the fact that this idea will not die is evidence enough that something must be there. That is my opinion on the "controversy."

When the Cal Tech group began their study they assumed that the apatite samples would reveal that Grand Canyon's rocks were buried in unequal amounts of overlying rock - unequal because the canyon today has 5,000 feet of relief and the lower samples should have been buried under more material than those collected from near the top. Most geologists suspect a very subdued surface over the canyon about 70 Ma. The illustration below (from my current lecture) shows red dots where the apatite samples were collected in eastern Grand Canyon. The unequal length of the blue arrows depicts the amount of overlying material they expected to find. 

After running the laboratory technique the samples produced surprising results to the researchers. They showed that no matter from what depth the samples were collected, they all appeared to have been buried under equal amounts of overlying rock. When the tops of the blue arrows are connected here, they reveal a canyon-like topography in eastern Grand Canyon about 70 Ma.

Below is a diagram that shows their interpretation of the data - a gorge of similar proportions was cut into the Mesozoic rocks that are now stripped back to the modern Echo and Vermilion Cliffs.

In my reading of the Science paper (not light I might add) I observed that the laboratory technique is not as evolved as one might hope for. Some assumptions are made that could result in different outcomes. Still, the technique has potential to help geologists better understand the erosional history of the area and even Karlstrom admits such a possibility. But he also wonders how a canyon could have been carved so early in time and then just sit there relatively unmodified for tens of millions of years. (Don Elston suspected that after being carved, the early canyon was partially filled with sediment and then exhumed only in the last 6 million years).

It's true that the Park will not soon change the widely regarded and useful date regarding the age of the Grand Canyon. What we see today from the canyon's edge is a gorge that has been greatly deepened and shaped in only the last few million years. The evolutionary history of the Colorado River shows that its exact course through the canyon to the Gulf of California was accomplished in only the last 6 million years. But as I make abundantly clear in "Carving Grand Canyon," most geologists too often conflate the age of the river with an absolute age for the canyon. For while the Colorado River is definitely no more than 6 million years old, the age of its ancestors or some early incarnation of the canyon need not be so strictly confined.

If we are to make sense of "When did the Grand Canyon form?" we should first ask ourselves, "What defines the Grand Canyon?" Karl Karlstrom and others say that the Grand Canyon must be a feature formed entirely by the modern Colorado River. I'm not so sure. Some aspects of the canyon, with respect to its depth or extent, could pre-date the modern river, having been formed by prior ancestors. Perhaps the question of "When did the Grand Canyon form?" can only be answered by another question: "What constitutes the beginning of the Grand Canyon?"

We are lucky that the world is paying us a visit at this time. Let us attempt to keep the debate civil, respectful, and without harsh words to our fellow geologists. We all seek the truth and each incremental step brings us closer to it. This is part of the process of getting to know a world-class landform that continues to inspire and enchant us all.