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Leave It To the Heat to Dull Autumn's Glory

Slashdot - 9 hours 33 min ago
It's autumn. Somebody tell the trees. From a report: Ordinarily, two signals alert deciduous trees that it's time to relinquish the green hues of summer in favor of autumn's yellows, oranges and reds. First, the days begin to grow shorter. Second, the temperature begins to drop. But this year, unseasonably warm weather across most of the U.S. has tricked trees into delaying the onset of fall's color extravaganza. Temperatures in the eastern half of the country have been as much as 15 degrees above normal since mid-September, and the warmth is expected to persist through the end of October. The unfortunate result for leaf peepers is a lackluster fall. Two kinds of pigments produce the season's liveliest foliage. Carotenoid, responsible for yellows and oranges, is always present in leaves but is usually masked by chlorophyll. The initial trigger for its appearance is shorter days. Anthocyanin, responsible for reds and deep purples, is different. Not all deciduous trees have this pigment, and those that do manufacture it from scratch in the fall. The primary trigger for its appearance is lower temperatures. Without that cooling cue, the colors of maple and other species that generally ignite New England with brilliant reds this time of year are likely to fizzle.

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Categories: Misc

Ohio sheriff's deputy resigns after racial slur accusation

Medina Gazette - 9 hours 42 min ago

SANDUSKY — An Ohio sheriff's deputy has resigned after being accused of using a racial slur at a Columbus bar.

Categories: Misc

Northwest Ohio head-on crash kills driver in car, newborn in SUV

Medina Gazette - 9 hours 42 min ago

BETTSVILLE — The State Highway Patrol says a head-on crash in northern Ohio killed a 6-week-old boy riding in an SUV and the 21-year-old driver who struck that vehicle.

Categories: Misc

Pruitt: If you want the EPA to enforce its own rules, you'll have to take us all the way to court

Daily Kos - 9 hours 46 min ago

Donald Trump’s Environmental Protection Agency head, Scott Pruitt, has found another way to gut the agency’s mission. Deriding the EPA’s practice of settling lawsuits brought by environmental groups trying to get it to enforce its own rules as “Sue & Settle,” Pruitt said the EPA wouldn’t be doing that anymore. 

The rule change could force environmental groups to spend much more time and effort on lawsuits aimed at making the EPA enforce its own rules and abide by agreed-upon timelines—spreading them thinner and making it harder for them to expend effort on other, more complicated cases. The EPA’s decision to refuse to reimburse lawyers’ fees also could be costly to environmental groups, as well as make it harder and less likely for average citizens and localities to undertake lawsuits to get the EPA to do what it’s legally required to do. [...]

The new memorandum formalizes a position of fighting every lawsuit tooth-and-nail that Pruitt had announced early in his tenure at the EPA. Back in February, he’d promised he wouldn’t allow “regulation through litigation.” The Justice Department also has stopped negotiating settlements that end up with payments to outside groups to cover attorneys’ or other fees.

In short, if you want the government to follow the rules, you had better have great lawyers and deep pockets, because you’re going to court. The Sierra Club fired back:

“Scott Pruitt and his polluter cronies continue to perpetrate lies about the law as an excuse for refusing enforcing it — but when it comes to the law, the truth has a way of catching up with you,” Sierra Club Environmental Law Program Director Pat Gallagher said in a statement. “If Pruitt thinks that by frivolously litigating deadline cases he will deter the Sierra Club or other citizen groups from holding him accountable in court, he should think again – we will not be deterred.”

But unless its donors step up in a big way—huge—even the Sierra Club is going to end up finding its resources strained in the fight to keep the Trump EPA from turning into the EDA (Environmental Destruction Agency).

Categories: Politics

Trump Takes No Blame For Legislative Failures: 'I'm Not Going To Blame Myself'

Crooks and Liars - 9 hours 47 min ago

During a quick presser before a cabinet meeting, when Trump was asked about his legislative failures, he took zero responsibility: "I’m not going to blame myself, I’ll be honest. They [Congress] are not getting the job done.”

Trump will always narcissistically avoid blame for any of his administration's shortcomings.

Karoli has a great post up detailing how Trump lied about cutting off ACA's subsidy monies and what it means. Are you surprised?

Trump was then asked about Steve Bannon's war on GOP and Leader Mitch McConnell.

He started off by saying what great relationships he has with the Senate and then backed up Bannon's point.

Trump said, "But but we're not getting the job done and I'm not going to blame myself. I'll be honest. They are not getting the job done."

He continued, "We've had health care approved and then you had a surprise vote by John McCain. We've had other things happen and they're not getting the job done and I can understand where Steve Bannon is coming from and I can understand, to be honest with you, John, I can understand where a lot of people are copping from because I'm not happy about it and a lot of people aren't happy about it."

Then he went on to say how "We need tax cuts."

In Trump's mind he's already the greatest president of all time and has done more in Congress than anyone.

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Categories: Politics

Trump still silent about actual American soldiers who died on his watch

Daily Kos - 9 hours 54 min ago

Donald Trump has his priorities.

One Week in Donald Trump's Twitter Feed Attacking Promoting Bragging About Free Press — 13 tweets Fox News — 4 tweets Himself — 8 tweets Democrats — 8 tweets Other Trumps — 3 tweets Stock Market — 7 tweets Healthcare — 6 tweets GOP candidates — 2 tweets Puerto Rico — 4 tweets Tax cuts — 2 tweets NFL — 4 tweets Las Vegas — 1 tweet Iran Treaty — 4 tweets Hillary Clinton — 1 tweet North Korea — 1 tweet Government — 1 tweet

While 69 tweets may seem like a lot, it clearly wasn’t enough to say anything about Puerto Rico other than how bad things were before the storms, or to say anything at all about the wildfires raging across California. 

Also missing in action on these tweets: any mention of American soldiers who were killed more than one week ago in Niger.

On Saturday October 7, the day the body of 25-year-old Army Sgt. La David Johnson was returned to Dover Air Force Base after he was killed in an ISIS ambush in Niger, President Donald Trump was golfing. It's not known if the President ever planned to attend the return of remains ceremony at Dover as he has in the past. But since the ambush on October 4 in Niger, he has not commented publicly on the deadliest combat incident involving US troops since he took office.

Trump has continued to carve out a slot between tee times for complaining about the NFL’s “disrespect” for soldiers. But he hasn’t freed up one second to discuss actual Green Berets actually dying on his watch.

Categories: Politics

Offensive overselling of the #microbiome in breast cancer from the Cleveland Clinic

The tree of life - 10 hours 4 min ago

This is just sickening to me.

I saw a news story that smelled funny:  Breast cancer: Bacterial deficiency linked with onset. And I went and found the scientific paper and then the press release from the Cleveland Clinic that the news story seemed based on.  And, well, the press release turns out to be ridiculous.

The paper showed something somewhat interesting but very limited.  Here is the abstract with key parts bolded and underlined by me
It has long been proposed that the gut microbiome contributes to breast carcinogenesis by modifying systemic estrogen levels. This is often cited as a possible mechanism linking breast cancer and high-fat, low-fiber diets as well as antibiotic exposure, associations previously identified in population-based studies. More recently, a distinct microbiome has been identified within breast milk and tissue, but few studies have characterized differences in the breast tissue microbiota of patients with and without cancer, and none have investigated distant body-site microbiomes outside of the gut. We hypothesize that cancerous breast tissue is associated with a microbiomic profile distinct from that of benign breast tissue, and that microbiomes of more distant sites, the oral cavity and urinary tract, will reflect dysbiosis as well. Fifty-seven women with invasive breast cancer undergoing mastectomy and 21 healthy women undergoing cosmetic breast surgery were enrolled. The bacterial 16S rRNA gene was amplified from urine, oral rinse and surgically collected breast tissue, sequenced, and processed through a QIIME-based bioinformatics pipeline. Cancer patient breast tissue microbiomes clustered significantly differently from non-cancer patients (p=0.03), largely driven by decreased relative abundance of Methylobacterium in cancer patients (median 0.10 vs. 0.24, p=0.03). There were no significant differences in oral rinse samples. Differences in urinary microbiomes were largely explained by menopausal status, with peri/postmenopausal women showing decreased levels of Lactobacillus. Independent of menopausal status, however, cancer patients had increased levels of gram-positive organisms including Corynebacterium (p<0.01), Staphylococcus (p=0.02), Actinomyces (p<0.01), and Propionibacteriaceae (p<0.01). Our observations suggest that the local breast microbiota differ in patients with and without breast cancer. Cancer patient urinary microbiomes were characterized by increased levels of gram-positive organisms in this study, but need to be further studied in larger cohorts.
That is it.  Barely significant finding of some clustering of the microbiomes of breast cancer patients versus those of patients without breast cancer.  And yet, this turned in the press release into cancer causing bacteria that they will be fighting with nanotechnology.  Seriously.

The press release title and subtitle is semi OK:
Cleveland Clinic Researchers Find Link Between Bacterial Imbalances and Breast Cancer. Study compares bacterial composition in healthy vs. cancerous breast tissue
But it goes way way way downhill from there.  Here are the parts with problems
  •  In our wildest dreams, we hope we can use microbiomics right before breast cancer forms and then prevent cancer with probiotics or antibiotics
    • Sure, in my wildest dreams I would cure cancer too.  
  • In addition to the Methylobacterium finding, the team discovered that cancer patients’ urine samples had increased levels of gram-positive bacteria, including Staphylococcus and Actinomyces. Further studies are needed to determine the role these organisms may play in breast cancer.
    • Umm.  No. Further studies are needed to see if these organisms play ANY role of any kind in breast cancer.
  • Co-senior author Stephen Grobymer, M.D., said, “If we can target specific pro-cancer bacteria, we may be able to make the environment less hospitable to cancer and enhance existing treatments. Larger studies are needed but this work is a solid first step in better understanding the significant role of bacterial imbalances in breast cancer.
    • Noooooooooooooooooooooooooooo.  You have not shown anywhere that there are "pro cancer" bacteria and this quote clearly implies that you have. 
  • The study provides proof-of-principle evidence to support further research into the creation and utilization of loaded submicroscopic particles (nanoparticles), targeting these pro-cancer bacteria. 
    • What?  This study does not provide ANY proof of principle of this sort.  You have not shown there are any pro-cancer bacteria.  This is ridiculous and offensive.  
No wonder the news stories imply that this study is about preventing breast cancer.  The press release from the Cleveland Clinic is deceptive.  It makes claims about the work that are irresponsible, misleading, and potentially dangerous. The Cleveland Clinic should be ashamed.

And thus the Cleveland Clinic is the winner of this edition of the Overselling the Microbiome Award.

UPDATE 10/16/17

And so the deceptive PR from Cleveland Clinic is now leading to claims of "Antibiotics May Prevent Breast Cancer" See

This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
Categories: Bio

Millions of High-Security Crypto Keys Crippled by Newly Discovered Flaw

Slashdot - 10 hours 13 min ago
Slovak and Czech researchers have found a vulnerability that leaves government and corporate encryption cards vulnerable to hackers to impersonate key owners, inject malicious code into digitally signed software, and decrypt sensitive data, reports ArsTechnica. From the report: The weakness allows attackers to calculate the private portion of any vulnerable key using nothing more than the corresponding public portion. Hackers can then use the private key to impersonate key owners, decrypt sensitive data, sneak malicious code into digitally signed software, and bypass protections that prevent accessing or tampering with stolen PCs. The five-year-old flaw is also troubling because it's located in code that complies with two internationally recognized security certification standards that are binding on many governments, contractors, and companies around the world. The code library was developed by German chipmaker Infineon and has been generating weak keys since 2012 at the latest. The flaw is the one Estonia's government obliquely referred to last month when it warned that 750,000 digital IDs issued since 2014 were vulnerable to attack. Estonian officials said they were closing the ID card public key database to prevent abuse. On Monday, officials posted this update. Last week, Microsoft, Google, and Infineon all warned how the weakness can impair the protections built into TPM products that ironically enough are designed to give an additional measure of security to high-targeted individuals and organizations.

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Categories: Misc

Trump Declares 'There Is No Such Thing As Obamacare Anymore'

Crooks and Liars - 10 hours 17 min ago

During today's (uncritically streamed by greedy cable networks) photo op with sycophants and bloodsuckers his cabinet, Donald Trump declared Obamacare dead.

"Obamacare is finished, it's dead, it's gone," Trump declared. "You shouldn't even mention it. It's gone. There is no such thing as Obamacare anymore."

He's absolutely right. When he signed the executive order raising premiums for everyone in order to take cost-sharing reduction assistance away from poor people, he ended any resemblance of the vision President Obama had for getting affordable healthcare to people.

This is TrumpCare, or perhaps more accurately, TrumpKills. So for one sentence buried in a giant pack of lies, Trump got something right.

But he got far more wrong, and intentionally so. He is lying when he says things like this:

"I knocked out the CSRs. That was a subsidy to the insurance companies. That was a gift that was frankly, what they gave the insurance companies just take a look at their stocks. Take a look where their stock was when Obamacare was originally approved and what it is today.

You'll see numbers that anybody if you invested in those stocks, you'd be extremely happy. And they have given them a total gift. They have given them you could almost call it a payoff. It's a disgrace. And that money goes to the insurance companies.

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Categories: Politics

Nature Publishing Group continues to deceive about #OpenAccess to genome papers

The tree of life - 10 hours 18 min ago
I was reminded today about the wonderful history of Nature in it's claim that it would make all papers reporting a new genome sequence freely and openly available. I wrote about how this was, well, not the truth, in 2012: The Tree of Life: Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh. And today I decided to recheck this.

So I searched for "Genome sequence" on the Nature site

And, well, I found a doozy of an example of a paper that is supposed to be openly available but is not. Initial sequencing and analysis of the human genome

That's right.  The "public" human genome paper is not freely or openly available.  It is $4.99 to rent or $20 to purchase.  Is this Nature's way of saying "We think the Lander et al. paper did not actually report on a genome?" and that the Venter paper truly won the race?  I don't think so.  I think this is a way of Nature saying "How can we make money off of our past papers? Which one gets a lot of looks? What? It is freely available? Change that." or something like that.

Want to bet they will say this is a mistake?  Want to bet they will not refund anybody's money who paid for this?

Here is a simple solution for everyone out there.  Do not trust Nature Publishing Group to make something available even if they say they will.

UPDATE 9/25 1 PM

But wait - there is more.  The Plasmodium genome paper, which I wrote about in 2012 not being available and which Nature promised to fix is again behind a pay wall

And more

UPDATE 10/16/17

Nature has apologized and said they fixed the issue and will refund any money people spent to buy these articles

This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter.
Categories: Bio

Reluctantly the panic begins to catch

Balloon Juice - 10 hours 25 min ago

It’s not often that I say this but good for Joe Manchin:

One Democratic senator called on Trump to withdraw the nomination of Rep. Tom Marino (R-Pa.) to lead the Office of National Drug Control Policy, a position requiring Senate confirmation. Another quickly introduced legislation to undo the law that Marino championed and that passed Congress with little opposition.

In a statement, Sen. Joe Manchin III (D-W.Va.) said he was “horrified” to read details of an investigation by The Washington Post and “60 Minutes” that detailed how a targeted lobbying effort helped weaken the Drug Enforcement Administration’s ability to go after drug distributors, even as opioid-related deaths continue to rise. He called on Trump to withdraw Marino’s nomination.

I assume the nomination will go through anyway.

And as opioids 100 people a day, Trump will do nothing. Eventually, there will be some symbolic bullshit that he’ll do that, that will make Fareed and Van Jones declare that he’s become presidential, but that’s about it.

Categories: Politics

Mike Pence Is A Calculating Gay-Bashing Koch-Toady, But You Knew That

Crooks and Liars - 10 hours 26 min ago
Mike Pence Is A Calculating Gay-Bashing Koch-Toady, But You Knew That

The New Yorker has taken the most un-NYer person alive, Mike Pence (A man so wooden that termites salivate when he enters a room), and profiles him. We presume they do this as some sort of lesson of what we may get when (?!) Trump is removed from office.

We present some clips:

  • Pence, who has dutifully stood by the President, mustering a devotional gaze rarely seen since the days of Nancy Reagan
  • Joel K. Goldstein, a historian and an expert on Vice-Presidents who teaches law at St. Louis University, refers to him as the “Sycophant-in-Chief.”
  • Pence exudes a low-key humility, but, McCawley told me, “he’s very ambitious, even calculating, about the steps he’ll take toward that goal.”
  • There was so little to do in the way of entertainment, (his brother) Gregory Pence recalled, that “we sometimes got in the car with our parents on Friday nights and followed after the fire truck.”
  • Mike Pence’s childhood nickname: Bubbles, because “he was chubby and funny.”

Mike ‘Payola’ Allen writing the Axios morning email thingie alerts us to a couple of passages in the article (which I have not finished reading) that might be considered warnings that Bubbles is exactly what we think he is:

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Categories: Politics

Report: T-Mobile and Sprint won’t sell off assets ahead of merger expected this month

9to5Mac - 10 hours 27 min ago

News today about the upcoming merger of T-Mobile and Sprint suggests that the two wireless providers won’t be selling any of their assets ahead of an announcement that could come as early as later this month.


Categories: Misc

Trump opened up a barrel of legal worms with his Obamacare sabotage

Daily Kos - 10 hours 28 min ago

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The attorneys general of eighteen states and the District of Columbia are now suing the Trump administration over his decision to suspend cost-sharing reduction payments, required by the Affordable Care Act, to health insurers to make health care more affordable for low-income people.

"By refusing to make the CSR reimbursement payments mandated by the ACA and its permanent appropriation," the states argue in their filing, "the President and the Secretaries are deliberately seeking to undermine, rather than faithfully execute, the ACA." It's entirely possible that health insurers will also file suit, as they are still required by the law to provide the subsidies to customers and the government is withholding the funds they're supposed to use to do that.

But there's another suit pending that could very well thwart Trump's sabotage of the CSR payments, ironically the suit that Trump is using as the excuse for his action.

For years, Republicans have argued that Congress never properly authorized the payments when it passed the Affordable Care Act in 2010, because it did not appropriate specific funds for them. The GOP-led House filed a lawsuit to that effect in 2014, and last year, U.S. District Court Judge Rosemary Collyer ruled in agreement, declaring the payments illegal but keeping them flowing pending an Obama administration appeal. In August, with the administration out of power, the U.S. Court of Appeals for the District of Columbia Circuit ruled that Democratic attorneys general could instead defend the subsidies in court. New York attorney general Eric Schneiderman has indicated that he will continue to pursue that litigation, but that Friday’s filing, seeking the injunction, will take precedence. Given that Collyer's punitive ruling came as a surprise to many legal observers, it's likely that other judges will disagree with her interpretation of the law.
Categories: Politics

Lunchtime Photo

Kevin Drum - 10 hours 38 min ago

ATTENTION! Our previously scheduled lunchtime photo has been postponed to bring you breaking news. EXCLUSIVE MUST CREDIT MOTHER JONES. Armageddon hit London today as the skies turned brown and the sun blazed a sullen orange at midday!

The Gherkin was so brown it looked like a cigar!

The Monument looked as if the city were on fire again!

The view from Earl’s Court tube station was Satanic!

These photos are unretouched, and no, I did not forget to reset the white balance on my camera. So what was going on? Apparently it was due to Britain catching the edge of Hurricane Ophelia:

According to the Met Office, the red sun is caused by winds pulling up Saharan dust….BBC weather presenter Simon King said: “Ophelia originated in the Azores where it was a hurricane and as it tracked its way northwards it dragged in tropical air from the Sahara….Because the dust is so high, light from the sun is scattered in the longer wavelengths, which is more the red part of the spectrum, so it appears red to our eyes.”

Ophelia has pulled in unseasonably warm air up from Spain and North Africa, bringing temperatures in the early 20s over the weekend….The air is safe to breathe, according to the Met Office, as the particles are high up in the atmosphere.

So there you have it. From London, I’m Kevin Drum reporting.

Categories: Politics

Apple releases third iOS 11.1, watchOS 4.1, and tvOS 11.1 betas [U]

9to5Mac - 10 hours 39 min ago

Update: Public betas for iOS and tvOS also now available.

Apple has released the third iOS 11.1 beta for iPhone and iPad. iOS 11.1 beta includes the return of 3D Touch gestures for multitasking as well as hundreds of new emoji characters including “Woman with Headscarf, Bearded Person, Breastfeeding, Zombie” and plenty more. Apple has also released the third beta versions of watchOS 4.1 beta with Apple Music and Radio streaming as well as tvOS 11.1 beta.


Categories: Misc

Trump on GOP healthcare fails: 'We're not getting the job done. And I'm not going to blame myself.'

Daily Kos - 10 hours 42 min ago

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Donald Trump showed just how much manure a lazy out-of-shape old man can shovel in a minute and a half at a cabinet meeting on Monday, from his own relationships with Senate Republicans to health care:

Despite what the press writes, I have great relationships with actually many senators, but in particular with most Republican senators. But we're not getting the job done. And I'm not going to blame myself. I'll be honest. They are not getting the job done.

We’re not—oh, who am I kidding, it’s not me, it’s them. But I have great relationships with them, the losers who are not getting the job done.

We’ve had health care approved and then you had the surprise vote by John McCain. We’ve had other things happen and they’re not getting the job done. And I can understand where Steve Bannon’s coming from and I can understand, to be honest with you John, I can understand where a lot of people are coming from. Because I’m not happy about it and a lot of people aren’t happy about it.

“Health care” by which he means the destruction of the system was approved except that it was not approved because of that one surprise vote that came in addition to the other two Republican votes that were not surprises. And it sure sounds like even if Bannon is no longer Trump’s top adviser, he has Trump’s approval in making war on the Republican establishment.

We need tax cuts. We need health care. Now, we’re going to get the health care done. In my opinion what’s happening is as we meet, Republicans are meeting with Democrats because of what I did with the CSRs, because I cut off the gravy train. If I didn’t cut the CSRs they wouldn’t be meeting, they’d be having lunch and enjoying themselves, all right? They’re right now having emergency meetings to get a short-term fix on health care, where premiums don’t have to double and triple like they’ve been doing under Obamacare.

Categories: Politics

Congressman Johnson: Pass the DREAM Act for future doctors like Cinthya

Daily Kos - 10 hours 45 min ago
Campaign Action

The dreams of Atlanta teen Cinthya Moran, who is dually enrolled in high school and college classes, stand to get derailed if Congress does not move on a passing the bipartisan DREAM Act, Congressman Hank Johnson writes. An estimated 100 DACA recipients are enrolled in medical schools around the country—including Denisse Rojas, who recently addressed Congress—and Cinthya is striving to join them:

As an aspiring cardiovascular surgeon, Cinthya took her studies seriously – accumulating a 3.8 GPA by staying up nights and studying – pushing herself to work twice as hard.

But now her dreams of becoming a doctor could be shattered forever.

That’s because Cinthya is one of about 800,000 DREAMers nationwide – young children brought to this country by their parents.

Thanks to President Trump’s craven decision to reverse the Deferred Action for Childhood Arrivals Program or DACA, Cinthya’s contributions and those of hundreds of thousands of other DREAMers to our community and country could come to an end.

Cinthya, 100 DACA medical students, and 800,000 others are at risk of being torn from the only country they’ve ever known as home following Jefferson Beauregard Sessions III announcing the end of the program. And despite Donald Trump’s claim, he can’t extend a program he’s already rescinded. Protecting undocumented immigrant youth like Cinthya is now in the hands of Congress. Johnson says:

Cinthya isn’t alone. DREAMers are models of what we hope our citizens become. They go to school, join the armed forces and become productive members of society. In Georgia, the rescission of DACA could mean that 24,000 people would be deported.

It is cruel to banish people to a strange land where oftentimes they don’t know the language or culture. It’s for constituents like Cinthya that I’m proud to join my Democratic colleagues in fighting to pass the DREAM Act.

”Cinthya has the potential, vision and dedication to become a cardiovascular surgeon,” Johnson writes, “but she wonders how she will be able to apply the knowledge and skills she has acquired ‘if I’m hiding away in fear of being taken back to a country I have no memory of?’” Cinthya and 800,000 undocumented immigrant youth like her need our help. Make a call to your member of Congress today and urge a clean vote on the bipartisan DREAM Act.

Categories: Politics